6-71543357-T-C

Variant names:

• chr6-71543357-T-C
• rs199630

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 0.622 in 151,902 control chromosomes in the GnomAD database, including 30,719 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 (30719 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.289

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.812 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: 0.622 AC: 94395 AN: 151784 Hom.: 30674 Cov.: 31

Gnomad AFR AF: 0.819

Gnomad AMI AF: 0.523

Gnomad AMR AF: 0.598

Gnomad ASJ AF: 0.454

Gnomad EAS AF: 0.686

Gnomad SAS AF: 0.634

Gnomad FIN AF: 0.513

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.529

Gnomad OTH AF: 0.596

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

GnomAD4 genome AF: 0.622 AC: 94498 AN: 151902 Hom.: 30719 Cov.: 31 AF XY: 0.623 AC XY: 46225 AN XY: 74220

Gnomad4 AFR AF: 0.820

Gnomad4 AMR AF: 0.598

Gnomad4 ASJ AF: 0.454

Gnomad4 EAS AF: 0.686

Gnomad4 SAS AF: 0.633

Gnomad4 FIN AF: 0.513

Gnomad4 NFE AF: 0.529

Gnomad4 OTH AF: 0.600

Alfa AF: 0.516 Hom.: 4431

Bravo AF: 0.637

Asia WGS AF: 0.694 AC: 2407 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.0
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs199630; hg19: chr6-72253060;