chr9-2241994-G-A

Variant names:

• chr9-2241994-G-A
• rs4741658
• ENST00000816246.1:n.675G>A

Variant summary

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

The ENST00000816246.1(ENSG00000306202):​n.675G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.247 in 152,094 control chromosomes in the GnomAD database, including 6,533 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 0.25 (6533 hom., cov: 32)
• Consequence: ENSG00000306202 ENST00000816246.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.582
• Publications: 3 publications found

Genes affected

ENSG00000306202 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.58).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.774 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107987043	XR_001746600.2	n.189+433C>T		intron_variant	Intron 1 of 3
LOC107987043	XR_007061395.1	n.193+433C>T		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000306202	ENST00000816246.1	n.675G>A		non_coding_transcript_exon_variant	Exon 1 of 3
ENSG00000306181	ENST00000816098.1	n.183+433C>T		intron_variant	Intron 1 of 4
ENSG00000306181	ENST00000816099.1	n.187+433C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.247 AC: 37531 AN: 151976 Hom.: 6529 Cov.: 32

Gnomad AFR AF: 0.0648

Gnomad AMI AF: 0.420

Gnomad AMR AF: 0.360

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.795

Gnomad SAS AF: 0.382

Gnomad FIN AF: 0.336

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.250

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

GnomAD4 genome AF: 0.247 AC: 37539 AN: 152094 Hom.: 6533 Cov.: 32 AF XY: 0.258 AC XY: 19196 AN XY: 74334

African (AFR) AF: 0.0646 AC: 2682 AN: 41548

American (AMR) AF: 0.360 AC: 5501 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.186 AC: 647 AN: 3470

East Asian (EAS) AF: 0.795 AC: 4073 AN: 5126

South Asian (SAS) AF: 0.381 AC: 1827 AN: 4794

European-Finnish (FIN) AF: 0.336 AC: 3553 AN: 10576

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.269 AC: 18306 AN: 67996

Other (OTH) AF: 0.253 AC: 533 AN: 2104

Alfa AF: 0.258 Hom.: 9289

Bravo AF: 0.244

Asia WGS AF: 0.523 AC: 1815 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	0.25
DANN	Benign	0.79
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs4741658; hg19: chr9-2241994; COSMIC: COSV69442576;