chr5-41587588-G-A

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 ENST00000742936.1(ENSG00000296840):​n.152G>A 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: ENSG00000296840 ENST00000742936.1 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000742936.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000251478	ENST00000504215.1	TSL:6	n.200C>T		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000296840	ENST00000742936.1		n.152G>A		non_coding_transcript_exon	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 v4.9

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;