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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374191	XR_001740998.2	n.290+11156C>A		intron_variant	Intron 1 of 3
LOC105374191	XR_001740999.3	n.290+11156C>A		intron_variant	Intron 1 of 3
LOC105374191	XR_001741000.2	n.290+11156C>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289884	ENST00000701346.1	n.258+11156C>A		intron_variant	Intron 1 of 5
ENSG00000289884	ENST00000702159.2	n.302+11156C>A		intron_variant	Intron 1 of 3
ENSG00000289884	ENST00000721983.1	n.84+11934C>A		intron_variant	Intron 1 of 3

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 v4.3

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

Other links and lift over

dbSNP: rs1708472; hg19: chr3-164180479; COSMIC: COSV50169118;