rs10274243

Positions:

• chr7-17364072-G-A

Variant summary

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

The XR_927074.3(LOC105375171):​n.212+244C>T 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 0.174 in 152,064 control chromosomes in the GnomAD database, including 3,034 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 0.17 (3034 hom., cov: 32)
• Consequence: LOC105375171 XR_927074.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25

Genes affected

LOC105375171 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.368 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105375171	XR_927074.3	n.212+244C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.174 AC: 26390 AN: 151946 Hom.: 3023 Cov.: 32

Gnomad AFR AF: 0.306

Gnomad AMI AF: 0.0954

Gnomad AMR AF: 0.137

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.382

Gnomad SAS AF: 0.158

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.147

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

GnomAD4 genome AF: 0.174 AC: 26440 AN: 152064 Hom.: 3034 Cov.: 32 AF XY: 0.174 AC XY: 12972 AN XY: 74342

Gnomad4 AFR AF: 0.307

Gnomad4 AMR AF: 0.137

Gnomad4 ASJ AF: 0.127

Gnomad4 EAS AF: 0.382

Gnomad4 SAS AF: 0.158

Gnomad4 FIN AF: 0.106

Gnomad4 NFE AF: 0.101

Gnomad4 OTH AF: 0.145

Alfa AF: 0.116 Hom.: 1190

Bravo AF: 0.183

Asia WGS AF: 0.231 AC: 800 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.034
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10274243; hg19: chr7-17403696;