rs1295371

Variant names:

• chr7-9816841-G-A
• rs1295371
• XR_927026.2:n.209+49949C>T

Your query was ambiguous. Multiple possible variants found:

• chr7-9816841-G-A
• chr7-9816841-G-C

Variant summary

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

The XR_927026.2(LOC105375147):​n.209+49949C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.228 in 151,956 control chromosomes in the GnomAD database, including 4,318 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 0.23 (4318 hom., cov: 32)
• Consequence: LOC105375147 XR_927026.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.695

Genes affected

LOC105375147 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.279 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375147	XR_927026.2	n.209+49949C>T		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.228 AC: 34597 AN: 151838 Hom.: 4313 Cov.: 32

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.334

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.203

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.300

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.283

Gnomad OTH AF: 0.227

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

GnomAD4 genome AF: 0.228 AC: 34611 AN: 151956 Hom.: 4318 Cov.: 32 AF XY: 0.226 AC XY: 16796 AN XY: 74262

Gnomad4 AFR AF: 0.118

Gnomad4 AMR AF: 0.241

Gnomad4 ASJ AF: 0.216

Gnomad4 EAS AF: 0.203

Gnomad4 SAS AF: 0.212

Gnomad4 FIN AF: 0.300

Gnomad4 NFE AF: 0.283

Gnomad4 OTH AF: 0.226

Alfa AF: 0.141 Hom.: 279

Bravo AF: 0.218

Asia WGS AF: 0.184 AC: 645 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.7
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1295371; hg19: chr7-9856470;