7-12207003-G-C

Variant names:

• chr7-12207003-G-C
• rs13244354

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 0.141 in 152,140 control chromosomes in the GnomAD database, including 1,715 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 0.14 (1715 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.928
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.208 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: 0.141 AC: 21403 AN: 152022 Hom.: 1712 Cov.: 32

Gnomad AFR AF: 0.212

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.0838

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.145

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.0713

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.141 AC: 21428 AN: 152140 Hom.: 1715 Cov.: 32 AF XY: 0.142 AC XY: 10550 AN XY: 74370

African (AFR) AF: 0.212 AC: 8770 AN: 41456

American (AMR) AF: 0.0836 AC: 1279 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.124 AC: 432 AN: 3472

East Asian (EAS) AF: 0.145 AC: 749 AN: 5176

South Asian (SAS) AF: 0.210 AC: 1011 AN: 4816

European-Finnish (FIN) AF: 0.0713 AC: 756 AN: 10606

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.117 AC: 7943 AN: 68002

Other (OTH) AF: 0.133 AC: 280 AN: 2110

Alfa AF: 0.0234 Hom.: 15

Bravo AF: 0.143

Asia WGS AF: 0.206 AC: 717 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.0
DANN	Benign	0.59
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs13244354; hg19: chr7-12246629;