rs9398840

Variant names:

• chr6-127348599-G-A
• rs9398840
• ENST00000761942.1:n.55+5148G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-127348599-G-A
• chr6-127348599-G-C

Variant summary

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

The ENST00000761942.1(ENSG00000299250):​n.55+5148G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.739 in 152,038 control chromosomes in the GnomAD database, including 41,678 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 0.74 (41678 hom., cov: 32)
• Consequence: ENSG00000299250 ENST00000761942.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.71
• Publications: 11 publications found

Genes affected

ENSG00000299250 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.759 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
ENSG00000299250	ENST00000761942.1	n.55+5148G>A		intron_variant	Intron 1 of 3
ENSG00000299250	ENST00000761943.1	n.129+4923G>A		intron_variant	Intron 1 of 3
ENSG00000299250	ENST00000761944.1	n.222+4923G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.739 AC: 112301 AN: 151920 Hom.: 41650 Cov.: 32

Gnomad AFR AF: 0.721

Gnomad AMI AF: 0.720

Gnomad AMR AF: 0.754

Gnomad ASJ AF: 0.762

Gnomad EAS AF: 0.779

Gnomad SAS AF: 0.619

Gnomad FIN AF: 0.725

Gnomad MID AF: 0.737

Gnomad NFE AF: 0.753

Gnomad OTH AF: 0.759

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

GnomAD4 genome AF: 0.739 AC: 112379 AN: 152038 Hom.: 41678 Cov.: 32 AF XY: 0.734 AC XY: 54529 AN XY: 74278

African (AFR) AF: 0.721 AC: 29924 AN: 41478

American (AMR) AF: 0.754 AC: 11518 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.762 AC: 2644 AN: 3470

East Asian (EAS) AF: 0.779 AC: 4018 AN: 5160

South Asian (SAS) AF: 0.619 AC: 2980 AN: 4816

European-Finnish (FIN) AF: 0.725 AC: 7639 AN: 10532

Middle Eastern (MID) AF: 0.738 AC: 217 AN: 294

European-Non Finnish (NFE) AF: 0.753 AC: 51187 AN: 67988

Other (OTH) AF: 0.758 AC: 1597 AN: 2108

Alfa AF: 0.748 Hom.: 133027

Bravo AF: 0.744

Asia WGS AF: 0.692 AC: 2409 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	0.40
DANN	Benign	0.61
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs9398840; hg19: chr6-127669744;