6-48964322-A-T

Variant names:

• chr6-48964322-A-T
• rs17637424

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0114 in 148,388 control chromosomes in the GnomAD database, including 182 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 0.011 (182 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.257
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0114 (1699/148388) while in subpopulation NFE AF = 0.0187 (1239/66360). AF 95% confidence interval is 0.0178. There are 182 homozygotes in GnomAd4. There are 827 alleles in the male GnomAd4 subpopulation. Median coverage is 30. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 182 gene

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: 0.0115 AC: 1703 AN: 148262 Hom.: 182 Cov.: 30

Gnomad AFR AF: 0.00305

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00557

Gnomad ASJ AF: 0.00378

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00990

Gnomad FIN AF: 0.0166

Gnomad MID AF: 0.0227

Gnomad NFE AF: 0.0187

Gnomad OTH AF: 0.00888

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

GnomAD4 genome AF: 0.0114 AC: 1699 AN: 148388 Hom.: 182 Cov.: 30 AF XY: 0.0114 AC XY: 827 AN XY: 72442

African (AFR) AF: 0.00304 AC: 124 AN: 40734

American (AMR) AF: 0.00556 AC: 83 AN: 14930

Ashkenazi Jewish (ASJ) AF: 0.00378 AC: 13 AN: 3436

East Asian (EAS) AF: 0.00 AC: 0 AN: 4898

South Asian (SAS) AF: 0.0101 AC: 45 AN: 4444

European-Finnish (FIN) AF: 0.0166 AC: 172 AN: 10354

Middle Eastern (MID) AF: 0.0174 AC: 5 AN: 288

European-Non Finnish (NFE) AF: 0.0187 AC: 1239 AN: 66360

Other (OTH) AF: 0.00879 AC: 18 AN: 2048

Alfa AF: 0.00582 Hom.: 15

Asia WGS AF: 0.00355 AC: 12 AN: 3390

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.1
DANN	Benign	0.27
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs17637424; hg19: chr6-48931959;