rs10212894

chr4-147080420-A-Gchr4-147080420-A-T

Variant summary

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

The ENST00000671296.1(ENSG00000286371):n.412+7194A>G 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 0.697 in 151,998 control chromosomes in the GnomAD database, including 37,560 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 0.70 (37560 hom., cov: 31)
• Consequence: ENST00000671296.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.55

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.773 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377476	XR_939316.3	n.352+7194A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000671296.1	n.412+7194A>G		intron_variant, non_coding_transcript_variant
	ENST00000667105.1	n.515+7194A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.697 AC: 105858 AN: 151880 Hom.: 37536 Cov.: 31

Gnomad AFR AF: 0.580

Gnomad AMI AF: 0.761

Gnomad AMR AF: 0.679

Gnomad ASJ AF: 0.621

Gnomad EAS AF: 0.581

Gnomad SAS AF: 0.678

Gnomad FIN AF: 0.748

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.778

Gnomad OTH AF: 0.681

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

GnomAD4 genome AF: 0.697 AC: 105924 AN: 151998 Hom.: 37560 Cov.: 31 AF XY: 0.695 AC XY: 51629 AN XY: 74296

Gnomad4 AFR AF: 0.580

Gnomad4 AMR AF: 0.678

Gnomad4 ASJ AF: 0.621

Gnomad4 EAS AF: 0.581

Gnomad4 SAS AF: 0.679

Gnomad4 FIN AF: 0.748

Gnomad4 NFE AF: 0.778

Gnomad4 OTH AF: 0.679

Alfa AF: 0.748 Hom.: 60125

Bravo AF: 0.682

Asia WGS AF: 0.624 AC: 2171 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.1
Dann	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10212894; hg19: chr4-148001572;