chr7-36038205-C-T

Position:

• chr7-36038205-C-T

Variant summary

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

The variant allele was found at a frequency of 0.311 in 152,144 control chromosomes in the GnomAD database, including 7,824 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 0.31 (7824 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.442

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.484 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.36038205C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000232930	ENST00000446024.1	n.459+2217C>T		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.311 AC: 47242 AN: 152026 Hom.: 7803 Cov.: 33

Gnomad AFR AF: 0.308

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.409

Gnomad ASJ AF: 0.254

Gnomad EAS AF: 0.476

Gnomad SAS AF: 0.500

Gnomad FIN AF: 0.320

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.304

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

GnomAD4 genome AF: 0.311 AC: 47320 AN: 152144 Hom.: 7824 Cov.: 33 AF XY: 0.320 AC XY: 23833 AN XY: 74370

Gnomad4 AFR AF: 0.309

Gnomad4 AMR AF: 0.410

Gnomad4 ASJ AF: 0.254

Gnomad4 EAS AF: 0.476

Gnomad4 SAS AF: 0.501

Gnomad4 FIN AF: 0.320

Gnomad4 NFE AF: 0.267

Gnomad4 OTH AF: 0.308

Alfa AF: 0.283 Hom.: 1099

Bravo AF: 0.315

Asia WGS AF: 0.466 AC: 1622 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.7
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10215376; hg19: chr7-36077815;