rs1631842

chr1-232311645-C-T

Variant summary

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

The XR_001738524.2(LOC101929902):n.711+1077G>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 0.372 in 152,066 control chromosomes in the GnomAD database, including 11,309 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 0.37 (11309 hom., cov: 32)
• Consequence: LOC101929902 XR_001738524.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.924

Genes affected

LOC101929902 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.448 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101929902	XR_001738524.2	n.711+1077G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.373 AC: 56606 AN: 151946 Hom.: 11312 Cov.: 32

Gnomad AFR AF: 0.250

Gnomad AMI AF: 0.459

Gnomad AMR AF: 0.365

Gnomad ASJ AF: 0.457

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.457

Gnomad FIN AF: 0.346

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.452

Gnomad OTH AF: 0.398

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

GnomAD4 genome AF: 0.372 AC: 56632 AN: 152066 Hom.: 11309 Cov.: 32 AF XY: 0.368 AC XY: 27370 AN XY: 74338

Gnomad4 AFR AF: 0.250

Gnomad4 AMR AF: 0.365

Gnomad4 ASJ AF: 0.457

Gnomad4 EAS AF: 0.216

Gnomad4 SAS AF: 0.456

Gnomad4 FIN AF: 0.346

Gnomad4 NFE AF: 0.452

Gnomad4 OTH AF: 0.401

Alfa AF: 0.439 Hom.: 29584

Bravo AF: 0.366

Asia WGS AF: 0.323 AC: 1130 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.66
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: rs1631842; hg19: chr1-232447391;