chr4-103580626-T-C

Variant names:

• chr4-103580626-T-C
• rs3857203
• ENST00000502936.1:n.190-10581T>C

Variant summary

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

The ENST00000502936.1(TACR3-AS1):​n.190-10581T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.511 in 152,094 control chromosomes in the GnomAD database, including 23,173 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 0.51 (23173 hom., cov: 33)
• Consequence: TACR3-AS1 ENST00000502936.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0770
• Publications: 0 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.64 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000502936.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TACR3-AS1	NR_186501.1		n.190-10581T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TACR3-AS1	ENST00000502936.1	TSL:2	n.190-10581T>C		intron	N/A
	TACR3-AS1	ENST00000512401.5	TSL:2	n.292-10581T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.511 AC: 77660 AN: 151976 Hom.: 23164 Cov.: 33

Gnomad AFR AF: 0.189

Gnomad AMI AF: 0.756

Gnomad AMR AF: 0.592

Gnomad ASJ AF: 0.667

Gnomad EAS AF: 0.490

Gnomad SAS AF: 0.443

Gnomad FIN AF: 0.757

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.645

Gnomad OTH AF: 0.535

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

GnomAD4 genome AF: 0.511 AC: 77692 AN: 152094 Hom.: 23173 Cov.: 33 AF XY: 0.516 AC XY: 38337 AN XY: 74340

African (AFR) AF: 0.189 AC: 7849 AN: 41508

American (AMR) AF: 0.592 AC: 9047 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.667 AC: 2316 AN: 3472

East Asian (EAS) AF: 0.489 AC: 2522 AN: 5160

South Asian (SAS) AF: 0.443 AC: 2134 AN: 4818

European-Finnish (FIN) AF: 0.757 AC: 8007 AN: 10580

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.645 AC: 43840 AN: 67960

Other (OTH) AF: 0.536 AC: 1130 AN: 2108

Alfa AF: 0.436 Hom.: 1544

Bravo AF: 0.490

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.59
PhyloP100		0.077

Splicing

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

Other links and lift over

dbSNP: rs3857203; hg19: chr4-104501783;