6-149113975-T-C

Position:

• chr6-149113975-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 0.428 in 151,938 control chromosomes in the GnomAD database, including 14,487 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 0.43 (14487 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0450

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.503 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.428 AC: 65022 AN: 151820 Hom.: 14466 Cov.: 32

Gnomad AFR AF: 0.509

Gnomad AMI AF: 0.466

Gnomad AMR AF: 0.296

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.436

Gnomad FIN AF: 0.489

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.424

Gnomad OTH AF: 0.399

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

GnomAD4 genome AF: 0.428 AC: 65092 AN: 151938 Hom.: 14487 Cov.: 32 AF XY: 0.429 AC XY: 31834 AN XY: 74242

Gnomad4 AFR AF: 0.509

Gnomad4 AMR AF: 0.296

Gnomad4 ASJ AF: 0.305

Gnomad4 EAS AF: 0.188

Gnomad4 SAS AF: 0.435

Gnomad4 FIN AF: 0.489

Gnomad4 NFE AF: 0.424

Gnomad4 OTH AF: 0.402

Alfa AF: 0.410 Hom.: 29009

Bravo AF: 0.411

Asia WGS AF: 0.413 AC: 1434 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.2
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7772697; hg19: chr6-149435111;