6-30978719-T-G

Variant names:

• chr6-30978719-T-G
• rs2844680

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 0.568 in 151,954 control chromosomes in the GnomAD database, including 24,652 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 0.57 (24652 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.341

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.573 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: 0.568 AC: 86217 AN: 151836 Hom.: 24645 Cov.: 31

Gnomad AFR AF: 0.575

Gnomad AMI AF: 0.692

Gnomad AMR AF: 0.582

Gnomad ASJ AF: 0.724

Gnomad EAS AF: 0.518

Gnomad SAS AF: 0.450

Gnomad FIN AF: 0.464

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.578

Gnomad OTH AF: 0.589

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

GnomAD4 genome AF: 0.568 AC: 86264 AN: 151954 Hom.: 24652 Cov.: 31 AF XY: 0.559 AC XY: 41479 AN XY: 74264

Gnomad4 AFR AF: 0.575

Gnomad4 AMR AF: 0.582

Gnomad4 ASJ AF: 0.724

Gnomad4 EAS AF: 0.518

Gnomad4 SAS AF: 0.448

Gnomad4 FIN AF: 0.464

Gnomad4 NFE AF: 0.578

Gnomad4 OTH AF: 0.588

Alfa AF: 0.580 Hom.: 20079

Bravo AF: 0.583

Asia WGS AF: 0.486 AC: 1691 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.2
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2844680; hg19: chr6-30946496;