6-44671447-T-C

Position:

• chr6-44671447-T-C

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 0.573 in 151,976 control chromosomes in the GnomAD database, including 25,821 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 0.57 (25821 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.516

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.883 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.573 AC: 87050 AN: 151858 Hom.: 25795 Cov.: 31

Gnomad AFR AF: 0.450

Gnomad AMI AF: 0.579

Gnomad AMR AF: 0.709

Gnomad ASJ AF: 0.618

Gnomad EAS AF: 0.904

Gnomad SAS AF: 0.585

Gnomad FIN AF: 0.605

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.583

Gnomad OTH AF: 0.601

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

GnomAD4 genome AF: 0.573 AC: 87125 AN: 151976 Hom.: 25821 Cov.: 31 AF XY: 0.578 AC XY: 42934 AN XY: 74276

Gnomad4 AFR AF: 0.450

Gnomad4 AMR AF: 0.709

Gnomad4 ASJ AF: 0.618

Gnomad4 EAS AF: 0.905

Gnomad4 SAS AF: 0.586

Gnomad4 FIN AF: 0.605

Gnomad4 NFE AF: 0.583

Gnomad4 OTH AF: 0.605

Alfa AF: 0.595 Hom.: 23622

Bravo AF: 0.577

Asia WGS AF: 0.720 AC: 2501 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.8
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11755164; hg19: chr6-44639184;