chr6-24028175-T-C

Variant names:

• chr6-24028175-T-C
• rs7761213

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 0.672 in 152,032 control chromosomes in the GnomAD database, including 34,482 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 0.67 (34482 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.38

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.71 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: 0.672 AC: 102124 AN: 151914 Hom.: 34448 Cov.: 32

Gnomad AFR AF: 0.654

Gnomad AMI AF: 0.816

Gnomad AMR AF: 0.721

Gnomad ASJ AF: 0.602

Gnomad EAS AF: 0.717

Gnomad SAS AF: 0.620

Gnomad FIN AF: 0.690

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.673

Gnomad OTH AF: 0.644

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

GnomAD4 genome AF: 0.672 AC: 102217 AN: 152032 Hom.: 34482 Cov.: 32 AF XY: 0.672 AC XY: 49898 AN XY: 74282

Gnomad4 AFR AF: 0.654

Gnomad4 AMR AF: 0.721

Gnomad4 ASJ AF: 0.602

Gnomad4 EAS AF: 0.718

Gnomad4 SAS AF: 0.620

Gnomad4 FIN AF: 0.690

Gnomad4 NFE AF: 0.673

Gnomad4 OTH AF: 0.644

Alfa AF: 0.670 Hom.: 69324

Bravo AF: 0.675

Asia WGS AF: 0.672 AC: 2340 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.17
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7761213; hg19: chr6-24028403;