rs994960

Variant names:

• chr3-73682765-G-A
• rs994960
• XR_001740755.1:n.351-4340C>T

Your query was ambiguous. Multiple possible variants found:

• chr3-73682765-G-A
• chr3-73682765-G-C
• chr3-73682765-G-T

Variant summary

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

The XR_001740755.1(LOC105377164):​n.351-4340C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.415 in 151,948 control chromosomes in the GnomAD database, including 14,717 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 0.41 (14717 hom., cov: 31)
• Consequence: LOC105377164 XR_001740755.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.957
• Publications: 4 publications found

Genes affected

LOC105377164 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.542 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377164	XR_001740755.1	n.351-4340C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.415 AC: 62994 AN: 151830 Hom.: 14711 Cov.: 31

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.499

Gnomad AMR AF: 0.463

Gnomad ASJ AF: 0.406

Gnomad EAS AF: 0.559

Gnomad SAS AF: 0.491

Gnomad FIN AF: 0.501

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.515

Gnomad OTH AF: 0.416

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

GnomAD4 genome AF: 0.415 AC: 63007 AN: 151948 Hom.: 14717 Cov.: 31 AF XY: 0.416 AC XY: 30912 AN XY: 74274

African (AFR) AF: 0.183 AC: 7570 AN: 41442

American (AMR) AF: 0.463 AC: 7062 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.406 AC: 1410 AN: 3472

East Asian (EAS) AF: 0.559 AC: 2878 AN: 5148

South Asian (SAS) AF: 0.492 AC: 2366 AN: 4806

European-Finnish (FIN) AF: 0.501 AC: 5279 AN: 10546

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.515 AC: 34969 AN: 67962

Other (OTH) AF: 0.420 AC: 885 AN: 2106

Alfa AF: 0.345 Hom.: 1733

Bravo AF: 0.400

Asia WGS AF: 0.498 AC: 1731 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.2
DANN	Benign	0.43
PhyloP100		0.96

Splicing

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

Other links and lift over

dbSNP: rs994960; hg19: chr3-73731916;