4-11673037-T-C

Variant names:

• chr4-11673037-T-C
• rs7671189
• ENST00000510095.5:n.98+47226T>C

Variant summary

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

The ENST00000510095.5(ENSG00000249631):​n.98+47226T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.724 in 152,068 control chromosomes in the GnomAD database, including 40,204 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 0.72 (40204 hom., cov: 32)
• Consequence: ENSG00000249631 ENST00000510095.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46
• Publications: 7 publications found

Genes affected

ENSG00000249631 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.802 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986178	NR_188483.1	n.268-97272T>C		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000249631	ENST00000510095.5	n.98+47226T>C		intron_variant	Intron 1 of 3	3

Frequencies

GnomAD3 genomes AF: 0.724 AC: 110046 AN: 151950 Hom.: 40176 Cov.: 32

Gnomad AFR AF: 0.810

Gnomad AMI AF: 0.471

Gnomad AMR AF: 0.637

Gnomad ASJ AF: 0.710

Gnomad EAS AF: 0.670

Gnomad SAS AF: 0.656

Gnomad FIN AF: 0.680

Gnomad MID AF: 0.741

Gnomad NFE AF: 0.712

Gnomad OTH AF: 0.718

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

GnomAD4 genome AF: 0.724 AC: 110139 AN: 152068 Hom.: 40204 Cov.: 32 AF XY: 0.720 AC XY: 53522 AN XY: 74310

African (AFR) AF: 0.810 AC: 33606 AN: 41510

American (AMR) AF: 0.637 AC: 9719 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.710 AC: 2463 AN: 3468

East Asian (EAS) AF: 0.671 AC: 3459 AN: 5154

South Asian (SAS) AF: 0.658 AC: 3176 AN: 4824

European-Finnish (FIN) AF: 0.680 AC: 7181 AN: 10564

Middle Eastern (MID) AF: 0.735 AC: 216 AN: 294

European-Non Finnish (NFE) AF: 0.712 AC: 48378 AN: 67968

Other (OTH) AF: 0.716 AC: 1511 AN: 2110

Alfa AF: 0.712 Hom.: 143314

Bravo AF: 0.723

Asia WGS AF: 0.671 AC: 2334 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.0
DANN	Benign	0.30
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs7671189; hg19: chr4-11674661;