rs1708472

Variant names:

• chr3-164462691-C-A
• rs1708472
• ENST00000701346.1:n.258+11156C>A

Your query was ambiguous. Multiple possible variants found:

• chr3-164462691-C-A
• chr3-164462691-C-G

Variant summary

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

The ENST00000701346.1(ENSG00000289884):​n.258+11156C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.5 in 151,968 control chromosomes in the GnomAD database, including 19,304 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 0.50 (19304 hom., cov: 33)
• Consequence: ENSG00000289884 ENST00000701346.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212
• Publications: 1 publications found

Genes affected

ENSG00000289884 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.568 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000701346.1. 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
	ENSG00000289884	ENST00000701346.1		n.258+11156C>A		intron	N/A
	ENSG00000289884	ENST00000702159.2		n.302+11156C>A		intron	N/A
	ENSG00000289884	ENST00000721983.1		n.84+11934C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.500 AC: 75978 AN: 151850 Hom.: 19276 Cov.: 33

Gnomad AFR AF: 0.574

Gnomad AMI AF: 0.497

Gnomad AMR AF: 0.556

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.345

Gnomad SAS AF: 0.389

Gnomad FIN AF: 0.511

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.463

Gnomad OTH AF: 0.492

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

GnomAD4 genome AF: 0.500 AC: 76055 AN: 151968 Hom.: 19304 Cov.: 33 AF XY: 0.500 AC XY: 37115 AN XY: 74298

African (AFR) AF: 0.574 AC: 23807 AN: 41454

American (AMR) AF: 0.557 AC: 8495 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.471 AC: 1635 AN: 3470

East Asian (EAS) AF: 0.344 AC: 1775 AN: 5154

South Asian (SAS) AF: 0.388 AC: 1869 AN: 4816

European-Finnish (FIN) AF: 0.511 AC: 5392 AN: 10556

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.463 AC: 31457 AN: 67944

Other (OTH) AF: 0.488 AC: 1028 AN: 2106

Alfa AF: 0.385 Hom.: 1151

Bravo AF: 0.510

Asia WGS AF: 0.360 AC: 1250 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.6
DANN	Benign	0.53
PhyloP100		0.21

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: rs1708472;

hg19: chr3-164180479;

COSMIC: COSV50169118;