rs7795573

Variant names:

• chr7-12880150-G-A
• rs7795573
• ENST00000638964.1:n.484+77418G>A

Your query was ambiguous. Multiple possible variants found:

• chr7-12880150-G-A
• chr7-12880150-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000638964.1(ENSG00000229618):​n.484+77418G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.26 in 151,826 control chromosomes in the GnomAD database, including 5,236 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 0.26 (5236 hom., cov: 32)
• Consequence: ENSG00000229618 ENST00000638964.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.135

Genes affected

ENSG00000229618 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.319 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
ENSG00000229618	ENST00000638964.1	n.484+77418G>A		intron_variant	Intron 1 of 5	5
ENSG00000229618	ENST00000639998.1	n.483+121834G>A		intron_variant	Intron 3 of 7	5

Frequencies

GnomAD3 genomes AF: 0.261 AC: 39523 AN: 151708 Hom.: 5241 Cov.: 32

Gnomad AFR AF: 0.262

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.143

Gnomad SAS AF: 0.333

Gnomad FIN AF: 0.305

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.265

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

GnomAD4 genome AF: 0.260 AC: 39540 AN: 151826 Hom.: 5236 Cov.: 32 AF XY: 0.264 AC XY: 19554 AN XY: 74184

Gnomad4 AFR AF: 0.262

Gnomad4 AMR AF: 0.211

Gnomad4 ASJ AF: 0.250

Gnomad4 EAS AF: 0.143

Gnomad4 SAS AF: 0.333

Gnomad4 FIN AF: 0.305

Gnomad4 NFE AF: 0.269

Gnomad4 OTH AF: 0.262

Alfa AF: 0.203 Hom.: 855

Bravo AF: 0.248

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.6
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7795573; hg19: chr7-12919775;