rs6971012

Variant names:

• chr7-97847950-T-C
• rs6971012

Variant summary

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

The variant allele was found at a frequency of 0.0492 in 152,292 control chromosomes in the GnomAD database, including 232 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 0.049 (232 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.084 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0493 AC: 7498 AN: 152174 Hom.: 232 Cov.: 32

Gnomad AFR AF: 0.0223

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.0408

Gnomad ASJ AF: 0.0421

Gnomad EAS AF: 0.0906

Gnomad SAS AF: 0.0406

Gnomad FIN AF: 0.0922

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0594

Gnomad OTH AF: 0.0353

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

GnomAD4 genome AF: 0.0492 AC: 7500 AN: 152292 Hom.: 232 Cov.: 32 AF XY: 0.0510 AC XY: 3794 AN XY: 74448

African (AFR) AF: 0.0223 AC: 927 AN: 41570

American (AMR) AF: 0.0408 AC: 625 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0421 AC: 146 AN: 3472

East Asian (EAS) AF: 0.0908 AC: 470 AN: 5178

South Asian (SAS) AF: 0.0404 AC: 195 AN: 4822

European-Finnish (FIN) AF: 0.0922 AC: 978 AN: 10606

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0594 AC: 4041 AN: 68022

Other (OTH) AF: 0.0350 AC: 74 AN: 2116

Alfa AF: 0.0549 Hom.: 29

Bravo AF: 0.0450

Asia WGS AF: 0.0610 AC: 215 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.14
DANN	Benign	0.67
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs6971012; hg19: chr7-97477262;