rs6962033

Variant names:

• chr7-134643618-G-A
• rs6962033
• XR_007060537.1:n.29222-23670C>T

Your query was ambiguous. Multiple possible variants found:

• chr7-134643618-G-A
• chr7-134643618-G-C

Variant summary

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

The XR_007060537.1(LOC124901750):​n.29222-23670C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.583 in 152,102 control chromosomes in the GnomAD database, including 26,893 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 0.58 (26893 hom., cov: 33)
• Consequence: LOC124901750 XR_007060537.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.273
• Publications: 4 publications found

Genes affected

LOC124901750 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.868 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901750	XR_007060537.1	n.29222-23670C>T		intron_variant	Intron 1 of 1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.583 AC: 88642 AN: 151982 Hom.: 26868 Cov.: 33

Gnomad AFR AF: 0.711

Gnomad AMI AF: 0.540

Gnomad AMR AF: 0.563

Gnomad ASJ AF: 0.506

Gnomad EAS AF: 0.889

Gnomad SAS AF: 0.718

Gnomad FIN AF: 0.534

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.491

Gnomad OTH AF: 0.550

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

GnomAD4 genome AF: 0.583 AC: 88726 AN: 152102 Hom.: 26893 Cov.: 33 AF XY: 0.590 AC XY: 43865 AN XY: 74350

African (AFR) AF: 0.711 AC: 29517 AN: 41490

American (AMR) AF: 0.563 AC: 8601 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.506 AC: 1756 AN: 3470

East Asian (EAS) AF: 0.889 AC: 4603 AN: 5178

South Asian (SAS) AF: 0.718 AC: 3461 AN: 4822

European-Finnish (FIN) AF: 0.534 AC: 5634 AN: 10556

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.491 AC: 33370 AN: 67986

Other (OTH) AF: 0.552 AC: 1164 AN: 2108

Alfa AF: 0.521 Hom.: 90499

Bravo AF: 0.589

Asia WGS AF: 0.763 AC: 2650 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.1
DANN	Benign	0.39
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs6962033; hg19: chr7-134328370;