rs10271989

Positions:

• chr7-131921403-G-A
• chr7-131921403-G-C
• chr7-131921403-G-T

Variant summary

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

The NR_110836.1(LOC101928782):​n.353-4836G>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 0.604 in 151,838 control chromosomes in the GnomAD database, including 30,917 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 0.60 (30917 hom., cov: 30)
• Consequence: LOC101928782 NR_110836.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.44

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.942 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC101928782	NR_110836.1	n.353-4836G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000415393.1	n.353-4836G>A		intron_variant, non_coding_transcript_variant		2
	ENST00000452219.5	n.86-10720G>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.604 AC: 91680 AN: 151722 Hom.: 30916 Cov.: 30

Gnomad AFR AF: 0.282

Gnomad AMI AF: 0.669

Gnomad AMR AF: 0.746

Gnomad ASJ AF: 0.634

Gnomad EAS AF: 0.965

Gnomad SAS AF: 0.683

Gnomad FIN AF: 0.714

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.714

Gnomad OTH AF: 0.646

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

GnomAD4 genome AF: 0.604 AC: 91697 AN: 151838 Hom.: 30917 Cov.: 30 AF XY: 0.612 AC XY: 45370 AN XY: 74188

Gnomad4 AFR AF: 0.282

Gnomad4 AMR AF: 0.746

Gnomad4 ASJ AF: 0.634

Gnomad4 EAS AF: 0.965

Gnomad4 SAS AF: 0.682

Gnomad4 FIN AF: 0.714

Gnomad4 NFE AF: 0.714

Gnomad4 OTH AF: 0.647

Alfa AF: 0.669 Hom.: 16838

Bravo AF: 0.593

Asia WGS AF: 0.760 AC: 2638 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	18
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: rs10271989; hg19: chr7-131606162;