17-40614034-T-C

Variant names:

• chr17-40614034-T-C
• rs7221109

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 0.682 in 151,922 control chromosomes in the GnomAD database, including 36,027 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 0.68 (36027 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.89
• Publications: 80 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.814 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: 0.682 AC: 103498 AN: 151804 Hom.: 35969 Cov.: 30

Gnomad AFR AF: 0.821

Gnomad AMI AF: 0.442

Gnomad AMR AF: 0.663

Gnomad ASJ AF: 0.544

Gnomad EAS AF: 0.772

Gnomad SAS AF: 0.586

Gnomad FIN AF: 0.600

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.628

Gnomad OTH AF: 0.624

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

GnomAD4 genome AF: 0.682 AC: 103625 AN: 151922 Hom.: 36027 Cov.: 30 AF XY: 0.678 AC XY: 50340 AN XY: 74242

African (AFR) AF: 0.821 AC: 33994 AN: 41404

American (AMR) AF: 0.663 AC: 10125 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.544 AC: 1888 AN: 3472

East Asian (EAS) AF: 0.772 AC: 3990 AN: 5166

South Asian (SAS) AF: 0.586 AC: 2817 AN: 4810

European-Finnish (FIN) AF: 0.600 AC: 6313 AN: 10530

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.628 AC: 42658 AN: 67962

Other (OTH) AF: 0.628 AC: 1327 AN: 2112

Alfa AF: 0.644 Hom.: 134838

Bravo AF: 0.696

Asia WGS AF: 0.698 AC: 2427 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.22
DANN	Benign	0.40
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs7221109; hg19: chr17-38770286;