rs163577

Variant names:

• chr3-3059103-T-C
• rs163577
• ENST00000442749.2:n.79+1964A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000442749.2(CNTN4-AS1):​n.79+1964A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.125 in 152,240 control chromosomes in the GnomAD database, including 1,257 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 0.12 (1257 hom., cov: 33)
  • Exomes 𝑓: 0.27 (0 hom.)
• Consequence: CNTN4-AS1 ENST00000442749.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.52
• Publications: 7 publications found

Genes affected

CNTN4-AS1 (HGNC:39985): (CNTN4 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.24).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.193 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CNTN4-AS1	NR_046554.1	n.79+1964A>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CNTN4-AS1	ENST00000442749.2	n.79+1964A>G		intron_variant	Intron 1 of 3	3
CNTN4-AS1	ENST00000629672.1	n.446+112A>G		intron_variant	Intron 3 of 3	5

Frequencies

GnomAD3 genomes AF: 0.125 AC: 18961 AN: 152092 Hom.: 1258 Cov.: 33

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.0603

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.0866

Gnomad SAS AF: 0.203

Gnomad FIN AF: 0.0693

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.138

GnomAD4 exome AF: 0.267 AC: 8 AN: 30 Hom.: 0 AF XY: 0.269 AC XY: 7 AN XY: 26

African (AFR) AF: 0.500 AC: 1 AN: 2

American (AMR) AF: 0.00 AC: 0 AN: 2

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.292 AC: 7 AN: 24

Other (OTH) AF: 0.00 AC: 0 AN: 2

GnomAD4 genome AF: 0.125 AC: 18965 AN: 152210 Hom.: 1257 Cov.: 33 AF XY: 0.124 AC XY: 9198 AN XY: 74420

African (AFR) AF: 0.130 AC: 5405 AN: 41504

American (AMR) AF: 0.119 AC: 1815 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.119 AC: 414 AN: 3472

East Asian (EAS) AF: 0.0864 AC: 447 AN: 5172

South Asian (SAS) AF: 0.203 AC: 980 AN: 4816

European-Finnish (FIN) AF: 0.0693 AC: 736 AN: 10616

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.129 AC: 8774 AN: 68010

Other (OTH) AF: 0.136 AC: 288 AN: 2112

Alfa AF: 0.132 Hom.: 2675

Bravo AF: 0.125

Asia WGS AF: 0.154 AC: 535 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.24
CADD	Benign	21
DANN	Benign	0.83
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs163577; hg19: chr3-3100787;