rs9501106

Variant names:

• chr6-31420332-G-A
• rs9501106
• ENST00000673857.1:n.62+19569G>A

Variant summary

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

The ENST00000673857.1(ENSG00000288587):​n.62+19569G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.216 in 151,528 control chromosomes in the GnomAD database, including 4,244 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 0.22 (4244 hom., cov: 31)
• Consequence: ENSG00000288587 ENST00000673857.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212
• Publications: 22 publications found

Genes affected

ENSG00000288587 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.309 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000673857.1. You can select a different transcript below to see updated ACMG assignments.

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
	ENSG00000288587	ENST00000673857.1		n.62+19569G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.216 AC: 32724 AN: 151408 Hom.: 4236 Cov.: 31

Gnomad AFR AF: 0.314

Gnomad AMI AF: 0.352

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.173

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.231

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.206

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

GnomAD4 genome AF: 0.216 AC: 32770 AN: 151528 Hom.: 4244 Cov.: 31 AF XY: 0.221 AC XY: 16389 AN XY: 74060

African (AFR) AF: 0.314 AC: 12918 AN: 41140

American (AMR) AF: 0.268 AC: 4070 AN: 15168

Ashkenazi Jewish (ASJ) AF: 0.276 AC: 955 AN: 3460

East Asian (EAS) AF: 0.174 AC: 898 AN: 5174

South Asian (SAS) AF: 0.227 AC: 1089 AN: 4804

European-Finnish (FIN) AF: 0.231 AC: 2432 AN: 10516

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.141 AC: 9592 AN: 67956

Other (OTH) AF: 0.203 AC: 428 AN: 2104

Alfa AF: 0.169 Hom.: 5512

Bravo AF: 0.222

Asia WGS AF: 0.197 AC: 684 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.9
DANN	Benign	0.74
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs9501106; hg19: chr6-31388109;