rs10954172

Positions:

• chr7-128223952-G-A
• chr7-128223952-G-T

Variant summary

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

The ENST00000692614.2(ENSG00000289434):​n.520-2412C>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 0.262 in 152,018 control chromosomes in the GnomAD database, including 6,089 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 0.26 (6089 hom., cov: 31)
• Consequence: ENST00000692614.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.379

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.375 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124901744	XR_007060516.1	n.781-81G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000692614.2	n.520-2412C>T		intron_variant, non_coding_transcript_variant
	ENST00000710955.1	n.836-81G>A		intron_variant, non_coding_transcript_variant
	ENST00000690022.1	n.244-2412C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.262 AC: 39852 AN: 151900 Hom.: 6082 Cov.: 31

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.438

Gnomad AMR AF: 0.382

Gnomad ASJ AF: 0.333

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.312

Gnomad FIN AF: 0.278

Gnomad MID AF: 0.217

Gnomad NFE AF: 0.319

Gnomad OTH AF: 0.258

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

GnomAD4 genome AF: 0.262 AC: 39883 AN: 152018 Hom.: 6089 Cov.: 31 AF XY: 0.264 AC XY: 19602 AN XY: 74296

Gnomad4 AFR AF: 0.117

Gnomad4 AMR AF: 0.383

Gnomad4 ASJ AF: 0.333

Gnomad4 EAS AF: 0.173

Gnomad4 SAS AF: 0.312

Gnomad4 FIN AF: 0.278

Gnomad4 NFE AF: 0.319

Gnomad4 OTH AF: 0.259

Alfa AF: 0.303 Hom.: 12441

Bravo AF: 0.266

Asia WGS AF: 0.246 AC: 856 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.4
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10954172; hg19: chr7-127864005;