6-10420248-G-C

Variant names:

• chr6-10420248-G-C
• rs303056

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 0.234 in 152,122 control chromosomes in the GnomAD database, including 8,669 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 0.23 (8669 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.718

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.612 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: 0.234 AC: 35533 AN: 152004 Hom.: 8644 Cov.: 33

Gnomad AFR AF: 0.618

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.0632

Gnomad EAS AF: 0.275

Gnomad SAS AF: 0.0870

Gnomad FIN AF: 0.0624

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.0675

Gnomad OTH AF: 0.203

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

GnomAD4 genome AF: 0.234 AC: 35600 AN: 152122 Hom.: 8669 Cov.: 33 AF XY: 0.228 AC XY: 16983 AN XY: 74334

Gnomad4 AFR AF: 0.618

Gnomad4 AMR AF: 0.142

Gnomad4 ASJ AF: 0.0632

Gnomad4 EAS AF: 0.275

Gnomad4 SAS AF: 0.0862

Gnomad4 FIN AF: 0.0624

Gnomad4 NFE AF: 0.0675

Gnomad4 OTH AF: 0.200

Alfa AF: 0.0343 Hom.: 44

Bravo AF: 0.259

Asia WGS AF: 0.189 AC: 660 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.3
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs303056; hg19: chr6-10420481;