22-38936618-C-T

Variant names:

• chr22-38936618-C-T
• rs1014971

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 0.545 in 152,038 control chromosomes in the GnomAD database, including 23,519 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 0.55 (23519 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.564
• Publications: 72 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 (NFE) allele frequency at 95% confidence interval = 0.637 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: 0.546 AC: 82906 AN: 151920 Hom.: 23520 Cov.: 32

Gnomad AFR AF: 0.422

Gnomad AMI AF: 0.502

Gnomad AMR AF: 0.523

Gnomad ASJ AF: 0.613

Gnomad EAS AF: 0.303

Gnomad SAS AF: 0.370

Gnomad FIN AF: 0.612

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.642

Gnomad OTH AF: 0.577

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

GnomAD4 genome AF: 0.545 AC: 82927 AN: 152038 Hom.: 23519 Cov.: 32 AF XY: 0.539 AC XY: 40066 AN XY: 74324

African (AFR) AF: 0.422 AC: 17499 AN: 41470

American (AMR) AF: 0.523 AC: 7986 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.613 AC: 2128 AN: 3472

East Asian (EAS) AF: 0.302 AC: 1562 AN: 5166

South Asian (SAS) AF: 0.371 AC: 1788 AN: 4820

European-Finnish (FIN) AF: 0.612 AC: 6465 AN: 10566

Middle Eastern (MID) AF: 0.650 AC: 191 AN: 294

European-Non Finnish (NFE) AF: 0.642 AC: 43642 AN: 67960

Other (OTH) AF: 0.575 AC: 1208 AN: 2102

Alfa AF: 0.610 Hom.: 115925

Bravo AF: 0.535

Asia WGS AF: 0.333 AC: 1162 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	1.5
DANN	Benign	0.71
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs1014971; hg19: chr22-39332623;