rs7314661

Variant names:

• chr12-670740-G-A
• rs7314661

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 0.164 in 152,190 control chromosomes in the GnomAD database, including 2,076 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 0.16 (2076 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.296
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.199 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: 0.164 AC: 25010 AN: 152072 Hom.: 2079 Cov.: 32

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.0614

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.191

Gnomad EAS AF: 0.0991

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.148

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

GnomAD4 genome AF: 0.164 AC: 25017 AN: 152190 Hom.: 2076 Cov.: 32 AF XY: 0.166 AC XY: 12337 AN XY: 74396

African (AFR) AF: 0.175 AC: 7277 AN: 41526

American (AMR) AF: 0.129 AC: 1972 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.191 AC: 662 AN: 3468

East Asian (EAS) AF: 0.0989 AC: 513 AN: 5186

South Asian (SAS) AF: 0.210 AC: 1013 AN: 4824

European-Finnish (FIN) AF: 0.192 AC: 2036 AN: 10590

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.164 AC: 11137 AN: 67992

Other (OTH) AF: 0.148 AC: 312 AN: 2112

Alfa AF: 0.161 Hom.: 9106

Bravo AF: 0.158

Asia WGS AF: 0.139 AC: 481 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	9.4
DANN	Benign	0.82
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs7314661; hg19: chr12-779906;