rs6919990

Positions:

• chr6-76674958-A-C
• chr6-76674958-A-G

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 0.118 in 152,120 control chromosomes in the GnomAD database, including 1,155 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 (1155 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0140

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.138 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17897 AN: 152002 Hom.: 1152 Cov.: 32

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.0241

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.0469

Gnomad EAS AF: 0.0149

Gnomad SAS AF: 0.0990

Gnomad FIN AF: 0.146

Gnomad MID AF: 0.0987

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.118 AC: 17911 AN: 152120 Hom.: 1155 Cov.: 32 AF XY: 0.118 AC XY: 8775 AN XY: 74374

Gnomad4 AFR AF: 0.141

Gnomad4 AMR AF: 0.126

Gnomad4 ASJ AF: 0.0469

Gnomad4 EAS AF: 0.0143

Gnomad4 SAS AF: 0.0988

Gnomad4 FIN AF: 0.146

Gnomad4 NFE AF: 0.112

Gnomad4 OTH AF: 0.107

Alfa AF: 0.111 Hom.: 479

Bravo AF: 0.116

Asia WGS AF: 0.0710 AC: 247 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.69
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6919990; hg19: chr6-77384675;