6-29821394-T-C

Variant names:

• chr6-29821394-T-C
• rs1610677

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 0.484 in 151,584 control chromosomes in the GnomAD database, including 17,946 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 0.48 (17946 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.645 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: 0.484 AC: 73307 AN: 151466 Hom.: 17923 Cov.: 31

Gnomad AFR AF: 0.509

Gnomad AMI AF: 0.459

Gnomad AMR AF: 0.514

Gnomad ASJ AF: 0.566

Gnomad EAS AF: 0.607

Gnomad SAS AF: 0.664

Gnomad FIN AF: 0.338

Gnomad MID AF: 0.586

Gnomad NFE AF: 0.458

Gnomad OTH AF: 0.499

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

GnomAD4 genome AF: 0.484 AC: 73370 AN: 151584 Hom.: 17946 Cov.: 31 AF XY: 0.484 AC XY: 35850 AN XY: 74070

Gnomad4 AFR AF: 0.509

Gnomad4 AMR AF: 0.513

Gnomad4 ASJ AF: 0.566

Gnomad4 EAS AF: 0.606

Gnomad4 SAS AF: 0.665

Gnomad4 FIN AF: 0.338

Gnomad4 NFE AF: 0.458

Gnomad4 OTH AF: 0.505

Alfa AF: 0.480 Hom.: 25093

Bravo AF: 0.496

Asia WGS AF: 0.682 AC: 2371 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.12
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1610677; hg19: chr6-29789171;