rs6909430

Variant names:

• chr6-98291898-G-A
• rs6909430
• ENST00000606913.5:n.344+16631G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-98291898-G-A
• chr6-98291898-G-C
• chr6-98291898-G-T

Variant summary

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

The ENST00000606913.5(ENSG00000271860):​n.344+16631G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.843 in 152,148 control chromosomes in the GnomAD database, including 54,316 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 0.84 (54316 hom., cov: 32)
• Consequence: ENSG00000271860 ENST00000606913.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.655
• Publications: 8 publications found

Genes affected

ENSG00000271860 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.88 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
ENSG00000271860	ENST00000606913.5	n.344+16631G>A		intron_variant	Intron 3 of 4	5
ENSG00000271860	ENST00000607032.1	n.515-666G>A		intron_variant	Intron 5 of 7	3
ENSG00000271860	ENST00000607823.5	n.560+12039G>A		intron_variant	Intron 6 of 6	5

Frequencies

GnomAD3 genomes AF: 0.843 AC: 128139 AN: 152030 Hom.: 54291 Cov.: 32

Gnomad AFR AF: 0.763

Gnomad AMI AF: 0.850

Gnomad AMR AF: 0.796

Gnomad ASJ AF: 0.910

Gnomad EAS AF: 0.842

Gnomad SAS AF: 0.901

Gnomad FIN AF: 0.921

Gnomad MID AF: 0.905

Gnomad NFE AF: 0.882

Gnomad OTH AF: 0.847

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

GnomAD4 genome AF: 0.843 AC: 128211 AN: 152148 Hom.: 54316 Cov.: 32 AF XY: 0.843 AC XY: 62694 AN XY: 74352

African (AFR) AF: 0.762 AC: 31625 AN: 41482

American (AMR) AF: 0.796 AC: 12141 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.910 AC: 3160 AN: 3472

East Asian (EAS) AF: 0.842 AC: 4348 AN: 5166

South Asian (SAS) AF: 0.902 AC: 4353 AN: 4826

European-Finnish (FIN) AF: 0.921 AC: 9776 AN: 10612

Middle Eastern (MID) AF: 0.901 AC: 265 AN: 294

European-Non Finnish (NFE) AF: 0.882 AC: 59978 AN: 68018

Other (OTH) AF: 0.848 AC: 1790 AN: 2112

Alfa AF: 0.822 Hom.: 25150

Bravo AF: 0.827

Asia WGS AF: 0.860 AC: 2991 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.70
DANN	Benign	0.48
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs6909430; hg19: chr6-98739774;