6-24646963-A-T

Variant names:

• chr6-24646963-A-T
• rs1883593

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 0.16 in 152,158 control chromosomes in the GnomAD database, including 2,028 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 0.16 (2028 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.226
• Publications: 5 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 = 0.188 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: 0.160 AC: 24307 AN: 152040 Hom.: 2026 Cov.: 33

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.0522

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.190

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.160 AC: 24332 AN: 152158 Hom.: 2028 Cov.: 33 AF XY: 0.154 AC XY: 11465 AN XY: 74406

African (AFR) AF: 0.152 AC: 6324 AN: 41498

American (AMR) AF: 0.116 AC: 1781 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.138 AC: 478 AN: 3468

East Asian (EAS) AF: 0.0521 AC: 270 AN: 5182

South Asian (SAS) AF: 0.117 AC: 565 AN: 4824

European-Finnish (FIN) AF: 0.131 AC: 1387 AN: 10596

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.190 AC: 12945 AN: 67986

Other (OTH) AF: 0.167 AC: 352 AN: 2102

Alfa AF: 0.178 Hom.: 317

Bravo AF: 0.158

Asia WGS AF: 0.105 AC: 365 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	1.4
DANN	Benign	0.81
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs1883593; hg19: chr6-24647191;