chr7-84801981-A-C

Variant names:

• chr7-84801981-A-C
• rs12707680

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 0.208 in 152,036 control chromosomes in the GnomAD database, including 3,281 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 0.21 (3281 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.182
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.223 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: 0.208 AC: 31529 AN: 151916 Hom.: 3272 Cov.: 32

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.192

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.199

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.242

Gnomad NFE AF: 0.226

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.208 AC: 31565 AN: 152036 Hom.: 3281 Cov.: 32 AF XY: 0.206 AC XY: 15342 AN XY: 74322

African (AFR) AF: 0.204 AC: 8476 AN: 41498

American (AMR) AF: 0.192 AC: 2928 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.192 AC: 667 AN: 3466

East Asian (EAS) AF: 0.153 AC: 791 AN: 5172

South Asian (SAS) AF: 0.198 AC: 955 AN: 4818

European-Finnish (FIN) AF: 0.162 AC: 1712 AN: 10558

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.226 AC: 15344 AN: 67930

Other (OTH) AF: 0.207 AC: 438 AN: 2114

Alfa AF: 0.221 Hom.: 1676

Bravo AF: 0.205

Asia WGS AF: 0.179 AC: 618 AN: 3448

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.8
DANN	Benign	0.72
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs12707680; hg19: chr7-84431297;