6-30124930-G-T

Variant names:

• chr6-30124930-G-T
• rs1419675

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 0.746 in 152,142 control chromosomes in the GnomAD database, including 42,597 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 0.75 (42597 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.285
• Publications: 30 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.862 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.746 AC: 113439 AN: 152024 Hom.: 42559 Cov.: 32

Gnomad AFR AF: 0.692

Gnomad AMI AF: 0.828

Gnomad AMR AF: 0.772

Gnomad ASJ AF: 0.693

Gnomad EAS AF: 0.884

Gnomad SAS AF: 0.780

Gnomad FIN AF: 0.846

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.748

Gnomad OTH AF: 0.713

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

GnomAD4 genome AF: 0.746 AC: 113534 AN: 152142 Hom.: 42597 Cov.: 32 AF XY: 0.750 AC XY: 55745 AN XY: 74372

African (AFR) AF: 0.692 AC: 28697 AN: 41470

American (AMR) AF: 0.772 AC: 11811 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.693 AC: 2403 AN: 3468

East Asian (EAS) AF: 0.884 AC: 4580 AN: 5182

South Asian (SAS) AF: 0.781 AC: 3768 AN: 4824

European-Finnish (FIN) AF: 0.846 AC: 8947 AN: 10580

Middle Eastern (MID) AF: 0.670 AC: 197 AN: 294

European-Non Finnish (NFE) AF: 0.748 AC: 50863 AN: 68002

Other (OTH) AF: 0.717 AC: 1513 AN: 2110

Alfa AF: 0.750 Hom.: 156371

Bravo AF: 0.735

Asia WGS AF: 0.842 AC: 2926 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	4.6
DANN	Benign	0.54
PhyloP100		0.28

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1419675;

hg19: chr6-30092707;