rs74141216

Positions:

• chr1-205448458-C-T

Variant summary

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

The NM_001397426.2(BLACAT1):​c.-36-7396G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.128 in 524,714 control chromosomes in the GnomAD database, including 4,646 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 0.14 (1551 hom., cov: 31)
  • Exomes 𝑓: 0.12 (3095 hom.)
• Consequence: BLACAT1 NM_001397426.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.82

Genes affected

BLACAT1 (HGNC:48597): (BLACAT1 overlapping LEMD1 locus)

LEMD1 (HGNC:18725): (LEM domain containing 1) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.185 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BLACAT1	NM_001397426.2	c.-36-7396G>A		intron_variant		ENST00000629624.3
BLACAT1	XM_047421189.1	c.-37+1410G>A		intron_variant
LEMD1	XM_047434586.1	c.-39+1410G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BLACAT1	ENST00000629624.3	c.-36-7396G>A		intron_variant		4	NM_001397426.2	P1

Frequencies

GnomAD3 genomes AF: 0.139 AC: 21095 AN: 151952 Hom.: 1552 Cov.: 31

Gnomad AFR AF: 0.188

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.0609

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.151

GnomAD4 exome AF: 0.124 AC: 46050 AN: 372644 Hom.: 3095 AF XY: 0.125 AC XY: 26532 AN XY: 212664

Gnomad4 AFR exome AF: 0.188

Gnomad4 AMR exome AF: 0.0977

Gnomad4 ASJ exome AF: 0.205

Gnomad4 EAS exome AF: 0.0533

Gnomad4 SAS exome AF: 0.129

Gnomad4 FIN exome AF: 0.152

Gnomad4 NFE exome AF: 0.117

Gnomad4 OTH exome AF: 0.130

GnomAD4 genome AF: 0.139 AC: 21114 AN: 152070 Hom.: 1551 Cov.: 31 AF XY: 0.140 AC XY: 10375 AN XY: 74344

Gnomad4 AFR AF: 0.188

Gnomad4 AMR AF: 0.112

Gnomad4 ASJ AF: 0.207

Gnomad4 EAS AF: 0.0610

Gnomad4 SAS AF: 0.121

Gnomad4 FIN AF: 0.159

Gnomad4 NFE AF: 0.117

Gnomad4 OTH AF: 0.149

Alfa AF: 0.125 Hom.: 164

Bravo AF: 0.137

Asia WGS AF: 0.0830 AC: 290 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	12
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs74141216; hg19: chr1-205417586;