rs9359271

Variant names:

• chr6-77456403-A-C
• rs9359271
• ENST00000741460.1:n.48+10497T>G

Your query was ambiguous. Multiple possible variants found:

• chr6-77456403-A-C
• chr6-77456403-A-T

Variant summary

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

The ENST00000741460.1(ENSG00000296734):​n.48+10497T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.355 in 151,992 control chromosomes in the GnomAD database, including 10,639 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 0.36 (10639 hom., cov: 32)
• Consequence: ENSG00000296734 ENST00000741460.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0390
• Publications: 7 publications found

Genes affected

ENSG00000296734 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.508 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377864	XM_047419660.1	c.-3743+14970A>C		intron_variant	Intron 5 of 8		XP_047275616.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000296734	ENST00000741460.1	n.48+10497T>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.355 AC: 53907 AN: 151874 Hom.: 10621 Cov.: 32

Gnomad AFR AF: 0.514

Gnomad AMI AF: 0.384

Gnomad AMR AF: 0.348

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.480

Gnomad SAS AF: 0.477

Gnomad FIN AF: 0.237

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.263

Gnomad OTH AF: 0.336

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

GnomAD4 genome AF: 0.355 AC: 53973 AN: 151992 Hom.: 10639 Cov.: 32 AF XY: 0.356 AC XY: 26483 AN XY: 74298

African (AFR) AF: 0.514 AC: 21292 AN: 41404

American (AMR) AF: 0.348 AC: 5313 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.310 AC: 1078 AN: 3472

East Asian (EAS) AF: 0.481 AC: 2476 AN: 5152

South Asian (SAS) AF: 0.478 AC: 2302 AN: 4820

European-Finnish (FIN) AF: 0.237 AC: 2512 AN: 10578

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.263 AC: 17856 AN: 67980

Other (OTH) AF: 0.335 AC: 708 AN: 2112

Alfa AF: 0.294 Hom.: 11787

Bravo AF: 0.367

Asia WGS AF: 0.451 AC: 1570 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.5
DANN	Benign	0.72
PhyloP100		0.039

Splicing

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

Other links and lift over

dbSNP: rs9359271; hg19: chr6-78166120;