6-153944390-G-C

Variant names:

• chr6-153944390-G-C
• rs605249

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 0.621 in 152,070 control chromosomes in the GnomAD database, including 29,490 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 0.62 (29490 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.112
• Publications: 2 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 = 0.675 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: 0.621 AC: 94329 AN: 151952 Hom.: 29469 Cov.: 32

Gnomad AFR AF: 0.573

Gnomad AMI AF: 0.670

Gnomad AMR AF: 0.526

Gnomad ASJ AF: 0.561

Gnomad EAS AF: 0.501

Gnomad SAS AF: 0.523

Gnomad FIN AF: 0.682

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.680

Gnomad OTH AF: 0.609

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

GnomAD4 genome AF: 0.621 AC: 94384 AN: 152070 Hom.: 29490 Cov.: 32 AF XY: 0.615 AC XY: 45711 AN XY: 74354

African (AFR) AF: 0.573 AC: 23755 AN: 41472

American (AMR) AF: 0.525 AC: 8023 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.561 AC: 1947 AN: 3468

East Asian (EAS) AF: 0.501 AC: 2597 AN: 5180

South Asian (SAS) AF: 0.524 AC: 2525 AN: 4820

European-Finnish (FIN) AF: 0.682 AC: 7196 AN: 10556

Middle Eastern (MID) AF: 0.690 AC: 203 AN: 294

European-Non Finnish (NFE) AF: 0.680 AC: 46252 AN: 67980

Other (OTH) AF: 0.605 AC: 1276 AN: 2110

Alfa AF: 0.639 Hom.: 3874

Bravo AF: 0.612

Asia WGS AF: 0.454 AC: 1582 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	1.3
DANN	Benign	0.37
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs605249; hg19: chr6-154265525;