rs7955901

Variant names:

• chr12-71039513-C-T
• rs7955901
• ENST00000548497.1:n.418-5265G>A

Variant summary

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

The ENST00000548497.1(ENSG00000257454):​n.418-5265G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.597 in 151,988 control chromosomes in the GnomAD database, including 28,068 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 0.60 (28068 hom., cov: 31)
• Consequence: ENSG00000257454 ENST00000548497.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.664

Genes affected

ENSG00000257454 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.743 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
ENSG00000257454	ENST00000548497.1	n.418-5265G>A		intron_variant	Intron 4 of 4	4

Frequencies

GnomAD3 genomes AF: 0.596 AC: 90573 AN: 151870 Hom.: 28023 Cov.: 31

Gnomad AFR AF: 0.750

Gnomad AMI AF: 0.454

Gnomad AMR AF: 0.482

Gnomad ASJ AF: 0.431

Gnomad EAS AF: 0.341

Gnomad SAS AF: 0.577

Gnomad FIN AF: 0.654

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.553

Gnomad OTH AF: 0.535

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

GnomAD4 genome AF: 0.597 AC: 90673 AN: 151988 Hom.: 28068 Cov.: 31 AF XY: 0.595 AC XY: 44184 AN XY: 74274

Gnomad4 AFR AF: 0.750

Gnomad4 AMR AF: 0.482

Gnomad4 ASJ AF: 0.431

Gnomad4 EAS AF: 0.341

Gnomad4 SAS AF: 0.576

Gnomad4 FIN AF: 0.654

Gnomad4 NFE AF: 0.553

Gnomad4 OTH AF: 0.534

Alfa AF: 0.566 Hom.: 11200

Bravo AF: 0.586

Asia WGS AF: 0.446 AC: 1556 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.72
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7955901; hg19: chr12-71433293;