chr7-95694611-G-A

Position:

• chr7-95694611-G-A

Variant summary

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

The XR_927774.3(LOC105375409):​n.177-22496G>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 0.377 in 151,486 control chromosomes in the GnomAD database, including 12,143 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 0.38 (12143 hom., cov: 31)
• Consequence: LOC105375409 XR_927774.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.13

Genes affected

LOC105375409 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.476 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375409	XR_927774.3	n.177-22496G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.378 AC: 57165 AN: 151368 Hom.: 12143 Cov.: 31

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.298

Gnomad AMR AF: 0.431

Gnomad ASJ AF: 0.495

Gnomad EAS AF: 0.279

Gnomad SAS AF: 0.452

Gnomad FIN AF: 0.444

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.480

Gnomad OTH AF: 0.391

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

GnomAD4 genome AF: 0.377 AC: 57167 AN: 151486 Hom.: 12143 Cov.: 31 AF XY: 0.378 AC XY: 27969 AN XY: 73952

Gnomad4 AFR AF: 0.167

Gnomad4 AMR AF: 0.431

Gnomad4 ASJ AF: 0.495

Gnomad4 EAS AF: 0.278

Gnomad4 SAS AF: 0.453

Gnomad4 FIN AF: 0.444

Gnomad4 NFE AF: 0.480

Gnomad4 OTH AF: 0.386

Alfa AF: 0.449 Hom.: 9420

Bravo AF: 0.370

Asia WGS AF: 0.359 AC: 1246 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	8.9
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs854100; hg19: chr7-95323923;