6-106693420-T-C

Variant names:

• chr6-106693420-T-C
• rs10499044

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.123 in 152,078 control chromosomes in the GnomAD database, including 1,318 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 0.12 (1318 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.380
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.213 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: 0.123 AC: 18678 AN: 151960 Hom.: 1319 Cov.: 32

Gnomad AFR AF: 0.0721

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.0750

Gnomad EAS AF: 0.201

Gnomad SAS AF: 0.224

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.123 AC: 18674 AN: 152078 Hom.: 1318 Cov.: 32 AF XY: 0.123 AC XY: 9120 AN XY: 74334

African (AFR) AF: 0.0719 AC: 2982 AN: 41486

American (AMR) AF: 0.111 AC: 1701 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0750 AC: 260 AN: 3466

East Asian (EAS) AF: 0.201 AC: 1038 AN: 5176

South Asian (SAS) AF: 0.224 AC: 1077 AN: 4812

European-Finnish (FIN) AF: 0.104 AC: 1095 AN: 10562

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.148 AC: 10060 AN: 67986

Other (OTH) AF: 0.136 AC: 287 AN: 2112

Alfa AF: 0.133 Hom.: 2684

Bravo AF: 0.118

Asia WGS AF: 0.225 AC: 784 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	6.1
DANN	Benign	0.83
PhyloP100		0.38

Splicing

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

Other links and lift over

dbSNP: rs10499044; hg19: chr6-107141295;