rs4274850

chr4-103579864-C-Achr4-103579864-C-T

Variant summary

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

The ENST00000502936.1(TACR3-AS1):n.190-11343C>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 0.874 in 152,168 control chromosomes in the GnomAD database, including 58,618 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 0.87 (58618 hom., cov: 31)
• Consequence: TACR3-AS1 ENST00000502936.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.797

Genes affected

TACR3-AS1 (HGNC:55593): (TACR3 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TACR3-AS1	ENST00000502936.1	n.190-11343C>A		intron_variant, non_coding_transcript_variant		2
TACR3-AS1	ENST00000512401.5	n.291+10462C>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.874 AC: 132943 AN: 152050 Hom.: 58556 Cov.: 31

Gnomad AFR AF: 0.965

Gnomad AMI AF: 0.929

Gnomad AMR AF: 0.870

Gnomad ASJ AF: 0.832

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.903

Gnomad FIN AF: 0.875

Gnomad MID AF: 0.880

Gnomad NFE AF: 0.810

Gnomad OTH AF: 0.877

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

GnomAD4 genome AF: 0.874 AC: 133063 AN: 152168 Hom.: 58618 Cov.: 31 AF XY: 0.880 AC XY: 65417 AN XY: 74368

Gnomad4 AFR AF: 0.965

Gnomad4 AMR AF: 0.870

Gnomad4 ASJ AF: 0.832

Gnomad4 EAS AF: 0.997

Gnomad4 SAS AF: 0.902

Gnomad4 FIN AF: 0.875

Gnomad4 NFE AF: 0.810

Gnomad4 OTH AF: 0.877

Alfa AF: 0.854 Hom.: 8064

Bravo AF: 0.879

Asia WGS AF: 0.941 AC: 3269 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.6
Dann	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4274850; hg19: chr4-104501021;