chr19-41925681-G-A

Variant names:

• chr19-41925681-G-A
• rs11665965
• NM_001365103.2:c.-14+2359C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001365103.2(ERFL):​c.-14+2359C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.685 in 151,852 control chromosomes in the GnomAD database, including 36,074 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.69 (36074 hom., cov: 30)
• Consequence: ERFL NM_001365103.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0120
• Publications: 11 publications found

Genes affected

ERFL (HGNC:53894): (ETS repressor factor like) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific. Predicted to be involved in cell differentiation and regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ARHGEF1 (HGNC:681): (Rho guanine nucleotide exchange factor 1) Rho GTPases play a fundamental role in numerous cellular processes that are initiated by extracellular stimuli that work through G protein coupled receptors. The encoded protein may form complex with G proteins and stimulate Rho-dependent signals. Multiple alternatively spliced transcript variants have been found for this gene, but the full-length nature of some variants has not been defined. [provided by RefSeq, Jul 2008]

ARHGEF1 Gene-Disease associations (from GenCC):

• immunodeficiency 62

  Inheritance: Unknown, AR Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae), ClinGen

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.8 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ERFL	NM_001365103.2	c.-14+2359C>T		intron_variant	Intron 1 of 5	ENST00000597630.3	NP_001352032.1
ARHGEF1	NM_001396003.1	c.2734+2448G>A		intron_variant	Intron 28 of 28		NP_001382932.1
ARHGEF1	NM_001396002.1	c.2635+2448G>A		intron_variant	Intron 27 of 27		NP_001382931.1
ARHGEF1	NR_173092.1	n.4373+2470G>A		intron_variant	Intron 30 of 30

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ERFL	ENST00000597630.3	c.-14+2359C>T		intron_variant	Intron 1 of 5	5	NM_001365103.2	ENSP00000491574.1

Frequencies

GnomAD3 genomes AF: 0.685 AC: 103997 AN: 151734 Hom.: 36043 Cov.: 30

Gnomad AFR AF: 0.764

Gnomad AMI AF: 0.654

Gnomad AMR AF: 0.645

Gnomad ASJ AF: 0.549

Gnomad EAS AF: 0.820

Gnomad SAS AF: 0.589

Gnomad FIN AF: 0.713

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.648

Gnomad OTH AF: 0.658

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.685 AC: 104069 AN: 151852 Hom.: 36074 Cov.: 30 AF XY: 0.684 AC XY: 50737 AN XY: 74202

African (AFR) AF: 0.763 AC: 31579 AN: 41368

American (AMR) AF: 0.644 AC: 9831 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.549 AC: 1903 AN: 3466

East Asian (EAS) AF: 0.820 AC: 4235 AN: 5162

South Asian (SAS) AF: 0.591 AC: 2837 AN: 4804

European-Finnish (FIN) AF: 0.713 AC: 7521 AN: 10554

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.648 AC: 44022 AN: 67932

Other (OTH) AF: 0.661 AC: 1393 AN: 2106

Alfa AF: 0.648 Hom.: 8774

Bravo AF: 0.687

Asia WGS AF: 0.708 AC: 2463 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.8
DANN	Benign	0.78
PhyloP100		0.012

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs11665965; hg19: chr19-42429833;