rs10241628

Variant names:

• chr7-55877867-A-G
• rs10241628
• ENST00000843355.1:n.331A>G

Variant summary

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

The ENST00000843355.1(ENSG00000309724):​n.331A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0336 in 672,468 control chromosomes in the GnomAD database, including 1,654 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 0.077 (1180 hom., cov: 33)
  • Exomes 𝑓: 0.021 (474 hom.)
• Consequence: ENSG00000309724 ENST00000843355.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.195
• Publications: 3 publications found

Genes affected

ENSG00000309724 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.225 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000843355.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000309724	ENST00000843355.1		n.331A>G		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000309724	ENST00000843356.1		n.248+81A>G		intron	N/A
	ENSG00000227499	ENST00000452998.1	TSL:6	n.-45A>G		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.0768 AC: 11682 AN: 152154 Hom.: 1175 Cov.: 33

Gnomad AFR AF: 0.230

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0424

Gnomad ASJ AF: 0.0150

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.00290

Gnomad FIN AF: 0.00631

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0183

Gnomad OTH AF: 0.0659

GnomAD4 exome AF: 0.0210 AC: 10902 AN: 520196 Hom.: 474 Cov.: 5 AF XY: 0.0193 AC XY: 5411 AN XY: 280472

African (AFR) AF: 0.227 AC: 3252 AN: 14316

American (AMR) AF: 0.0262 AC: 770 AN: 29358

Ashkenazi Jewish (ASJ) AF: 0.0157 AC: 238 AN: 15202

East Asian (EAS) AF: 0.00 AC: 0 AN: 33554

South Asian (SAS) AF: 0.00233 AC: 125 AN: 53676

European-Finnish (FIN) AF: 0.00731 AC: 334 AN: 45712

Middle Eastern (MID) AF: 0.0311 AC: 95 AN: 3050

European-Non Finnish (NFE) AF: 0.0178 AC: 5299 AN: 297720

Other (OTH) AF: 0.0286 AC: 789 AN: 27608

GnomAD4 genome AF: 0.0768 AC: 11702 AN: 152272 Hom.: 1180 Cov.: 33 AF XY: 0.0740 AC XY: 5509 AN XY: 74450

African (AFR) AF: 0.229 AC: 9524 AN: 41526

American (AMR) AF: 0.0423 AC: 647 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0150 AC: 52 AN: 3472

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5186

South Asian (SAS) AF: 0.00311 AC: 15 AN: 4828

European-Finnish (FIN) AF: 0.00631 AC: 67 AN: 10618

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0183 AC: 1245 AN: 68030

Other (OTH) AF: 0.0652 AC: 138 AN: 2116

Alfa AF: 0.0509 Hom.: 88

Bravo AF: 0.0855

Asia WGS AF: 0.0160 AC: 55 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	3.5
DANN	Benign	0.52
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs10241628; hg19: chr7-55945560;