10-7112902-G-T

Position:

• chr10-7112902-G-T

Variant summary

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

The ENST00000664549.1(ENSG00000287277):​n.190+5378C>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 0.232 in 152,092 control chromosomes in the GnomAD database, including 5,046 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 (5046 hom., cov: 31)
• Consequence: ENST00000664549.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.304

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.33 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105376387	XR_007062046.1	n.363+6729C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000664549.1	n.190+5378C>A		intron_variant, non_coding_transcript_variant
	ENST00000666104.1	n.135+5378C>A		intron_variant, non_coding_transcript_variant
	ENST00000668409.1	n.153+5378C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.232 AC: 35216 AN: 151974 Hom.: 5044 Cov.: 31

Gnomad AFR AF: 0.0779

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.314

Gnomad EAS AF: 0.0937

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.264

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

GnomAD4 genome AF: 0.232 AC: 35216 AN: 152092 Hom.: 5046 Cov.: 31 AF XY: 0.226 AC XY: 16824 AN XY: 74346

Gnomad4 AFR AF: 0.0777

Gnomad4 AMR AF: 0.227

Gnomad4 ASJ AF: 0.314

Gnomad4 EAS AF: 0.0941

Gnomad4 SAS AF: 0.163

Gnomad4 FIN AF: 0.249

Gnomad4 NFE AF: 0.333

Gnomad4 OTH AF: 0.261

Alfa AF: 0.313 Hom.: 11132

Bravo AF: 0.226

Asia WGS AF: 0.115 AC: 398 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.4
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10905106; hg19: chr10-7154864;