rs7955901

Positions:

• chr12-71039513-C-T

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, non coding transcript 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: ENST00000548497.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.664

Genes affected

(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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000548497.1	n.418-5265G>A		intron_variant, non_coding_transcript_variant		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;