7-95396848-G-C

Position:

• chr7-95396848-G-C

Variant summary

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

The ENST00000702974.1(ENSG00000290101):​n.352G>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.186 in 152,196 control chromosomes in the GnomAD database, including 3,622 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 0.19 (3622 hom., cov: 32)
• Consequence: ENST00000702974.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.567 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107986822	XR_007060439.1	n.377G>C		non_coding_transcript_exon_variant	1/2
LOC107986822	XR_001745283.2	n.377G>C		non_coding_transcript_exon_variant	1/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000702974.1	n.352G>C		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.186 AC: 28252 AN: 152076 Hom.: 3618 Cov.: 32

Gnomad AFR AF: 0.0664

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.332

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.585

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.186 AC: 28262 AN: 152196 Hom.: 3622 Cov.: 32 AF XY: 0.192 AC XY: 14262 AN XY: 74402

Gnomad4 AFR AF: 0.0663

Gnomad4 AMR AF: 0.332

Gnomad4 ASJ AF: 0.215

Gnomad4 EAS AF: 0.585

Gnomad4 SAS AF: 0.257

Gnomad4 FIN AF: 0.156

Gnomad4 NFE AF: 0.194

Gnomad4 OTH AF: 0.209

Alfa AF: 0.170 Hom.: 318

Bravo AF: 0.198

Asia WGS AF: 0.385 AC: 1337 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.0
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2072200; hg19: chr7-95026160;