rs1387837

Positions:

• chr10-18714164-G-A
• chr10-18714164-G-C
• chr10-18714164-G-T

Variant summary

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

The ENST00000654305.1(ENSG00000234244):​n.93+3803G>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 0.563 in 151,872 control chromosomes in the GnomAD database, including 24,860 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 0.56 (24860 hom., cov: 31)
• Consequence: ENST00000654305.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.272

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.71 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105376440	XR_930721.2	n.68+3803G>A		intron_variant, non_coding_transcript_variant
LOC105376440	XR_930720.2	n.51+3803G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000654305.1	n.93+3803G>A		intron_variant, non_coding_transcript_variant
	ENST00000654415.1	n.78+3803G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.563 AC: 85472 AN: 151754 Hom.: 24823 Cov.: 31

Gnomad AFR AF: 0.717

Gnomad AMI AF: 0.722

Gnomad AMR AF: 0.543

Gnomad ASJ AF: 0.441

Gnomad EAS AF: 0.549

Gnomad SAS AF: 0.377

Gnomad FIN AF: 0.478

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.508

Gnomad OTH AF: 0.519

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

GnomAD4 genome AF: 0.563 AC: 85559 AN: 151872 Hom.: 24860 Cov.: 31 AF XY: 0.557 AC XY: 41358 AN XY: 74230

Gnomad4 AFR AF: 0.717

Gnomad4 AMR AF: 0.543

Gnomad4 ASJ AF: 0.441

Gnomad4 EAS AF: 0.549

Gnomad4 SAS AF: 0.376

Gnomad4 FIN AF: 0.478

Gnomad4 NFE AF: 0.508

Gnomad4 OTH AF: 0.513

Alfa AF: 0.503 Hom.: 38783

Bravo AF: 0.582

Asia WGS AF: 0.477 AC: 1659 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	8.2
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1387837; hg19: chr10-19003093;