rs4252051

Variant names:

• chr6-160701184-T-C
• rs4252051
• ENST00000448126.6:n.980T>C

Your query was ambiguous. Multiple possible variants found:

• chr6-160701184-T-C
• chr6-160701184-T-G

Variant summary

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

The ENST00000448126.6(ENSG00000224477):​n.980T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 152,088 control chromosomes in the GnomAD database, including 1,113 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 0.11 (1113 hom., cov: 32)
• Consequence: ENSG00000224477 ENST00000448126.6 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.93
• Publications: 4 publications found

Genes affected

ENSG00000224477 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.158 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000224477	ENST00000448126.6	n.980T>C		non_coding_transcript_exon_variant	Exon 2 of 2	5

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16655 AN: 151970 Hom.: 1110 Cov.: 32

Gnomad AFR AF: 0.0304

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.00444

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.0953

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

GnomAD4 genome AF: 0.110 AC: 16665 AN: 152088 Hom.: 1113 Cov.: 32 AF XY: 0.107 AC XY: 7972 AN XY: 74364

African (AFR) AF: 0.0303 AC: 1257 AN: 41528

American (AMR) AF: 0.113 AC: 1722 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.150 AC: 520 AN: 3472

East Asian (EAS) AF: 0.00445 AC: 23 AN: 5174

South Asian (SAS) AF: 0.127 AC: 612 AN: 4808

European-Finnish (FIN) AF: 0.116 AC: 1229 AN: 10580

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.161 AC: 10919 AN: 67934

Other (OTH) AF: 0.0943 AC: 199 AN: 2110

Alfa AF: 0.0677 Hom.: 84

Bravo AF: 0.104

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.18
DANN	Benign	0.17
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs4252051; hg19: chr6-161122216;