6-44628604-T-C

Variant names:

• chr6-44628604-T-C
• rs632728

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 0.752 in 151,970 control chromosomes in the GnomAD database, including 43,974 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 0.75 (43974 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.947
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.901 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: 0.752 AC: 114244 AN: 151852 Hom.: 43929 Cov.: 34

Gnomad AFR AF: 0.909

Gnomad AMI AF: 0.843

Gnomad AMR AF: 0.689

Gnomad ASJ AF: 0.696

Gnomad EAS AF: 0.532

Gnomad SAS AF: 0.736

Gnomad FIN AF: 0.667

Gnomad MID AF: 0.797

Gnomad NFE AF: 0.704

Gnomad OTH AF: 0.756

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

GnomAD4 genome AF: 0.752 AC: 114351 AN: 151970 Hom.: 43974 Cov.: 34 AF XY: 0.748 AC XY: 55549 AN XY: 74274

African (AFR) AF: 0.909 AC: 37702 AN: 41484

American (AMR) AF: 0.689 AC: 10531 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.696 AC: 2415 AN: 3468

East Asian (EAS) AF: 0.532 AC: 2751 AN: 5168

South Asian (SAS) AF: 0.737 AC: 3551 AN: 4820

European-Finnish (FIN) AF: 0.667 AC: 7011 AN: 10518

Middle Eastern (MID) AF: 0.799 AC: 235 AN: 294

European-Non Finnish (NFE) AF: 0.704 AC: 47792 AN: 67914

Other (OTH) AF: 0.755 AC: 1594 AN: 2110

Alfa AF: 0.718 Hom.: 52449

Bravo AF: 0.757

Asia WGS AF: 0.661 AC: 2302 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.3
DANN	Benign	0.80
PhyloP100		-0.95

Splicing

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

Other links and lift over

dbSNP: rs632728; hg19: chr6-44596341;