chr7-17683648-A-G

Variant names:

• chr7-17683648-A-G
• rs13222101

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 0.119 in 152,172 control chromosomes in the GnomAD database, including 1,145 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 0.12 (1145 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.825
• Publications: 3 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 (NFE) allele frequency at 95% confidence interval = 0.146 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: 0.119 AC: 18045 AN: 152054 Hom.: 1143 Cov.: 32

Gnomad AFR AF: 0.0801

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.0468

Gnomad SAS AF: 0.0888

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.119 AC: 18037 AN: 152172 Hom.: 1145 Cov.: 32 AF XY: 0.118 AC XY: 8761 AN XY: 74372

African (AFR) AF: 0.0798 AC: 3317 AN: 41542

American (AMR) AF: 0.106 AC: 1623 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.104 AC: 360 AN: 3470

East Asian (EAS) AF: 0.0467 AC: 242 AN: 5182

South Asian (SAS) AF: 0.0888 AC: 428 AN: 4818

European-Finnish (FIN) AF: 0.150 AC: 1593 AN: 10588

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.148 AC: 10075 AN: 67980

Other (OTH) AF: 0.116 AC: 244 AN: 2108

Alfa AF: 0.137 Hom.: 2462

Bravo AF: 0.111

Asia WGS AF: 0.101 AC: 352 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	0.41
DANN	Benign	0.47
PhyloP100		-0.82

Splicing

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

Other links and lift over

dbSNP: rs13222101; hg19: chr7-17723272;