chr6-153944390-G-C

Variant names:

• chr6-153944390-G-C
• rs605249

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.573

Gnomad4 AMR AF: 0.525

Gnomad4 ASJ AF: 0.561

Gnomad4 EAS AF: 0.501

Gnomad4 SAS AF: 0.524

Gnomad4 FIN AF: 0.682

Gnomad4 NFE AF: 0.680

Gnomad4 OTH AF: 0.605

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs605249; hg19: chr6-154265525;