7-35361837-T-C

Position:

• chr7-35361837-T-C

Variant summary

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

The NR_038864.1(LOC401324):​n.187+9446T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.726 in 151,842 control chromosomes in the GnomAD database, including 40,417 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 0.73 (40417 hom., cov: 30)
• Consequence: LOC401324 NR_038864.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.310

Genes affected

ENSG00000287651 (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 (EAS) allele frequency at 95% confidence interval = 0.816 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC401324	NR_038864.1	n.187+9446T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000287651	ENST00000656715.1	n.204+9446T>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.726 AC: 110191 AN: 151724 Hom.: 40393 Cov.: 30

Gnomad AFR AF: 0.812

Gnomad AMI AF: 0.592

Gnomad AMR AF: 0.682

Gnomad ASJ AF: 0.662

Gnomad EAS AF: 0.837

Gnomad SAS AF: 0.692

Gnomad FIN AF: 0.680

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.691

Gnomad OTH AF: 0.698

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

GnomAD4 genome AF: 0.726 AC: 110266 AN: 151842 Hom.: 40417 Cov.: 30 AF XY: 0.724 AC XY: 53742 AN XY: 74198

Gnomad4 AFR AF: 0.812

Gnomad4 AMR AF: 0.682

Gnomad4 ASJ AF: 0.662

Gnomad4 EAS AF: 0.837

Gnomad4 SAS AF: 0.691

Gnomad4 FIN AF: 0.680

Gnomad4 NFE AF: 0.691

Gnomad4 OTH AF: 0.697

Alfa AF: 0.698 Hom.: 58454

Bravo AF: 0.727

Asia WGS AF: 0.738 AC: 2565 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	5.9
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2392362; hg19: chr7-35401447;