rs4274850

Variant names:

• chr4-103579864-C-A
• rs4274850
• ENST00000502936.1:n.190-11343C>A

Your query was ambiguous. Multiple possible variants found:

• chr4-103579864-C-A
• chr4-103579864-C-T

Variant summary

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

The ENST00000502936.1(TACR3-AS1):​n.190-11343C>A variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.797
• Publications: 3 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
TACR3-AS1	NR_186501.1	n.190-11343C>A		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TACR3-AS1	ENST00000502936.1	n.190-11343C>A		intron_variant	Intron 2 of 4	2
TACR3-AS1	ENST00000512401.5	n.291+10462C>A		intron_variant	Intron 3 of 4	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

African (AFR) AF: 0.965 AC: 40111 AN: 41548

American (AMR) AF: 0.870 AC: 13292 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.832 AC: 2888 AN: 3472

East Asian (EAS) AF: 0.997 AC: 5171 AN: 5188

South Asian (SAS) AF: 0.902 AC: 4344 AN: 4814

European-Finnish (FIN) AF: 0.875 AC: 9247 AN: 10570

Middle Eastern (MID) AF: 0.874 AC: 257 AN: 294

European-Non Finnish (NFE) AF: 0.810 AC: 55053 AN: 67984

Other (OTH) AF: 0.877 AC: 1853 AN: 2112

Alfa AF: 0.857 Hom.: 17625

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
PhyloP100		0.80

Splicing

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

Other links and lift over

dbSNP: rs4274850; hg19: chr4-104501021;