rs6972823

Variant names:

• chr7-3196264-T-A
• rs6972823
• XR_007060192.1:n.1057A>T

Variant summary

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

The XR_007060192.1(LOC124901574):​n.1057A>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.636 in 152,014 control chromosomes in the GnomAD database, including 31,274 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 0.64 (31274 hom., cov: 32)
• Consequence: LOC124901574 XR_007060192.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0520
• Publications: 3 publications found

Genes affected

LOC124901574 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.752 is higher than 0.05.

Variant Effect in Transcripts

 

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
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.636 AC: 96555 AN: 151896 Hom.: 31240 Cov.: 32

Gnomad AFR AF: 0.759

Gnomad AMI AF: 0.650

Gnomad AMR AF: 0.629

Gnomad ASJ AF: 0.529

Gnomad EAS AF: 0.649

Gnomad SAS AF: 0.500

Gnomad FIN AF: 0.635

Gnomad MID AF: 0.526

Gnomad NFE AF: 0.577

Gnomad OTH AF: 0.614

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

GnomAD4 genome AF: 0.636 AC: 96640 AN: 152014 Hom.: 31274 Cov.: 32 AF XY: 0.635 AC XY: 47202 AN XY: 74292

African (AFR) AF: 0.759 AC: 31464 AN: 41464

American (AMR) AF: 0.629 AC: 9602 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.529 AC: 1834 AN: 3466

East Asian (EAS) AF: 0.649 AC: 3354 AN: 5166

South Asian (SAS) AF: 0.500 AC: 2410 AN: 4816

European-Finnish (FIN) AF: 0.635 AC: 6698 AN: 10552

Middle Eastern (MID) AF: 0.521 AC: 151 AN: 290

European-Non Finnish (NFE) AF: 0.577 AC: 39238 AN: 67972

Other (OTH) AF: 0.614 AC: 1296 AN: 2110

Alfa AF: 0.612 Hom.: 3564

Bravo AF: 0.640

Asia WGS AF: 0.630 AC: 2192 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.4
DANN	Benign	0.50
PhyloP100		0.052

Splicing

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

Other links and lift over

dbSNP: rs6972823; hg19: chr7-3235896;