rs662204

Variant names:

• chr5-41587588-G-A
• rs662204
• ENST00000504215.1:n.200C>T

Variant summary

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

The ENST00000504215.1(ENSG00000251478):​n.200C>T variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.0917 in 688,522 control chromosomes in the GnomAD database, including 4,541 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 0.10 (966 hom., cov: 33)
  • Exomes 𝑓: 0.088 (3575 hom.)
• Consequence: ENSG00000251478 ENST00000504215.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.50
• Publications: 2 publications found

Genes affected

ENSG00000251478 (HGNC:):

TCP1P2 (HGNC:11660):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.174 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TCP1P2		n.41587588G>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000251478	ENST00000504215.1	n.200C>T		non_coding_transcript_exon_variant	Exon 1 of 2	6
ENSG00000296840	ENST00000742936.1	n.152G>A		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15697 AN: 151998 Hom.: 964 Cov.: 33

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.0451

Gnomad AMR AF: 0.0845

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.00407

Gnomad SAS AF: 0.0635

Gnomad FIN AF: 0.0507

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.0802

Gnomad OTH AF: 0.111

GnomAD4 exome AF: 0.0884 AC: 47416 AN: 536406 Hom.: 3575 Cov.: 0 AF XY: 0.0877 AC XY: 25914 AN XY: 295470

African (AFR) AF: 0.196 AC: 3043 AN: 15492

American (AMR) AF: 0.0854 AC: 3494 AN: 40898

Ashkenazi Jewish (ASJ) AF: 0.136 AC: 2457 AN: 18114

East Asian (EAS) AF: 0.00690 AC: 163 AN: 23614

South Asian (SAS) AF: 0.0780 AC: 5377 AN: 68922

European-Finnish (FIN) AF: 0.0591 AC: 2740 AN: 46396

Middle Eastern (MID) AF: 0.132 AC: 277 AN: 2102

European-Non Finnish (NFE) AF: 0.0922 AC: 27087 AN: 293680

Other (OTH) AF: 0.102 AC: 2778 AN: 27188

GnomAD4 genome AF: 0.103 AC: 15700 AN: 152116 Hom.: 966 Cov.: 33 AF XY: 0.101 AC XY: 7479 AN XY: 74344

African (AFR) AF: 0.178 AC: 7371 AN: 41474

American (AMR) AF: 0.0843 AC: 1289 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.120 AC: 416 AN: 3470

East Asian (EAS) AF: 0.00408 AC: 21 AN: 5150

South Asian (SAS) AF: 0.0627 AC: 302 AN: 4818

European-Finnish (FIN) AF: 0.0507 AC: 536 AN: 10574

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.0803 AC: 5459 AN: 68024

Other (OTH) AF: 0.109 AC: 231 AN: 2112

Alfa AF: 0.104 Hom.: 128

Bravo AF: 0.110

Asia WGS AF: 0.0500 AC: 174 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	5.9
DANN	Benign	0.26
PhyloP100		4.5

Splicing

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

Other links and lift over

dbSNP: rs662204; hg19: chr5-41587690;