4-83170698-T-C

Variant names:

• chr4-83170698-T-C
• rs4693570
• ENST00000809763.1:n.262+170A>G

Variant summary

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

The ENST00000809763.1(ENSG00000305249):​n.262+170A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.556 in 151,890 control chromosomes in the GnomAD database, including 24,306 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 0.56 (24306 hom., cov: 31)
• Consequence: ENSG00000305249 ENST00000809763.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.453
• Publications: 10 publications found

Genes affected

ENSG00000305249 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.689 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124900167	XR_007058167.1	n.1446+18279A>G		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000305249	ENST00000809763.1	n.262+170A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.557 AC: 84468 AN: 151772 Hom.: 24286 Cov.: 31

Gnomad AFR AF: 0.410

Gnomad AMI AF: 0.489

Gnomad AMR AF: 0.654

Gnomad ASJ AF: 0.570

Gnomad EAS AF: 0.700

Gnomad SAS AF: 0.709

Gnomad FIN AF: 0.633

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.591

Gnomad OTH AF: 0.552

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

GnomAD4 genome AF: 0.556 AC: 84526 AN: 151890 Hom.: 24306 Cov.: 31 AF XY: 0.563 AC XY: 41785 AN XY: 74232

African (AFR) AF: 0.409 AC: 16945 AN: 41382

American (AMR) AF: 0.655 AC: 9996 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.570 AC: 1975 AN: 3466

East Asian (EAS) AF: 0.699 AC: 3611 AN: 5166

South Asian (SAS) AF: 0.709 AC: 3423 AN: 4826

European-Finnish (FIN) AF: 0.633 AC: 6656 AN: 10520

Middle Eastern (MID) AF: 0.544 AC: 160 AN: 294

European-Non Finnish (NFE) AF: 0.591 AC: 40147 AN: 67956

Other (OTH) AF: 0.555 AC: 1170 AN: 2108

Alfa AF: 0.569 Hom.: 40682

Bravo AF: 0.549

Asia WGS AF: 0.709 AC: 2468 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.1
DANN	Benign	0.50
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs4693570; hg19: chr4-84091851;