rs3106134

Variant names:

• chr4-94206940-A-G
• rs3106134
• ENST00000501965.2:n.27+590T>C

Your query was ambiguous. Multiple possible variants found:

• chr4-94206940-A-G
• chr4-94206940-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000501965.2(SMARCAD1-DT):​n.27+590T>C variant causes a intron 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 ENST00000501965.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.729
• Publications: 4 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SMARCAD1-DT	NR_125922.1	n.27+590T>C		intron_variant	Intron 1 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SMARCAD1-DT	ENST00000501965.2	n.27+590T>C		intron_variant	Intron 1 of 8	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

African (AFR) AF: 0.357 AC: 14773 AN: 41374

American (AMR) AF: 0.503 AC: 7680 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.395 AC: 1369 AN: 3470

East Asian (EAS) AF: 0.715 AC: 3690 AN: 5162

South Asian (SAS) AF: 0.594 AC: 2860 AN: 4812

European-Finnish (FIN) AF: 0.387 AC: 4080 AN: 10532

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.403 AC: 27397 AN: 67960

Other (OTH) AF: 0.415 AC: 874 AN: 2104

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
PhyloP100		0.73

Splicing

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

Other links and lift over

dbSNP: rs3106134; hg19: chr4-95128091;