rs3106134

chr4-94206940-A-Gchr4-94206940-A-T

Variant summary

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

The NR_125922.1(SMARCAD1-DT):n.27+590T>C 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 0.416 in 151,874 control chromosomes in the GnomAD database, including 13,646 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 0.42 (13646 hom., cov: 31)
• Consequence: SMARCAD1-DT NR_125922.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.729

Genes affected

SMARCAD1-DT (HGNC:53364): (SMARCAD1 divergent transcript)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.696 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SMARCAD1-DT	NR_125922.1	n.27+590T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SMARCAD1-DT	ENST00000501965.2	n.27+590T>C		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.416 AC: 63181 AN: 151756 Hom.: 13624 Cov.: 31

Gnomad AFR AF: 0.357

Gnomad AMI AF: 0.418

Gnomad AMR AF: 0.502

Gnomad ASJ AF: 0.395

Gnomad EAS AF: 0.716

Gnomad SAS AF: 0.594

Gnomad FIN AF: 0.387

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.403

Gnomad OTH AF: 0.408

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

GnomAD4 genome AF: 0.416 AC: 63229 AN: 151874 Hom.: 13646 Cov.: 31 AF XY: 0.423 AC XY: 31391 AN XY: 74202

Gnomad4 AFR AF: 0.357

Gnomad4 AMR AF: 0.503

Gnomad4 ASJ AF: 0.395

Gnomad4 EAS AF: 0.715

Gnomad4 SAS AF: 0.594

Gnomad4 FIN AF: 0.387

Gnomad4 NFE AF: 0.403

Gnomad4 OTH AF: 0.415

Alfa AF: 0.399 Hom.: 1987

Bravo AF: 0.423

Asia WGS AF: 0.640 AC: 2226 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
Cadd	Benign	11
Dann	Benign	0.94

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3106134; hg19: chr4-95128091;