6-61265489-G-C

Variant names:

• chr6-61265489-G-C
• rs1689237

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 0.604 in 151,742 control chromosomes in the GnomAD database, including 28,032 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 0.60 (28032 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0520

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 = 0.654 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: 0.604 AC: 91650 AN: 151624 Hom.: 28018 Cov.: 30

Gnomad AFR AF: 0.662

Gnomad AMI AF: 0.697

Gnomad AMR AF: 0.599

Gnomad ASJ AF: 0.490

Gnomad EAS AF: 0.526

Gnomad SAS AF: 0.425

Gnomad FIN AF: 0.496

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.612

Gnomad OTH AF: 0.592

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

GnomAD4 genome AF: 0.604 AC: 91692 AN: 151742 Hom.: 28032 Cov.: 30 AF XY: 0.592 AC XY: 43919 AN XY: 74148

Gnomad4 AFR AF: 0.661

Gnomad4 AMR AF: 0.599

Gnomad4 ASJ AF: 0.490

Gnomad4 EAS AF: 0.526

Gnomad4 SAS AF: 0.425

Gnomad4 FIN AF: 0.496

Gnomad4 NFE AF: 0.612

Gnomad4 OTH AF: 0.590

Alfa AF: 0.463 Hom.: 1188

Bravo AF: 0.619

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.27
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1689237; hg19: chr6-61972225;