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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000809763.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000305249	ENST00000809763.1		n.262+170A>G		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4693570;

hg19: chr4-84091851;