ENST00000419326.1:n.471G>C

Variant names:

• chr7-36755819-G-C
• rs11977641
• ENST00000419326.1:n.471G>C

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

The ENST00000419326.1(ENSG00000229424):​n.471G>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. 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 0.0098 (13 hom., cov: 20)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000229424 ENST00000419326.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0960
• Publications: 3 publications found

Genes affected

ENSG00000229424 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BS2: High Homozygotes in GnomAd4 at 13 gene

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
ENSG00000229424	ENST00000419326.1	n.471G>C		non_coding_transcript_exon_variant	Exon 2 of 3	4
ENSG00000307889	ENST00000829619.1	n.182-15482C>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.00985 AC: 733 AN: 74400 Hom.: 13 Cov.: 20

Gnomad AFR AF: 0.0314

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00403

Gnomad ASJ AF: 0.00229

Gnomad EAS AF: 0.00998

Gnomad SAS AF: 0.00114

Gnomad FIN AF: 0.000862

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00130

Gnomad OTH AF: 0.00382

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 142 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 112

African (AFR) AC: 0 AN: 0

American (AMR) AF: 0.00 AC: 0 AN: 4

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AF: 0.00 AC: 0 AN: 4

South Asian (SAS) AF: 0.00 AC: 0 AN: 18

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 6

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 98

Other (OTH) AF: 0.00 AC: 0 AN: 8

GnomAD4 genome AF: 0.00984 AC: 733 AN: 74460 Hom.: 13 Cov.: 20 AF XY: 0.00986 AC XY: 348 AN XY: 35290

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.0314 AC: 633 AN: 20168

American (AMR) AF: 0.00403 AC: 30 AN: 7444

Ashkenazi Jewish (ASJ) AF: 0.00229 AC: 4 AN: 1750

East Asian (EAS) AF: 0.0101 AC: 10 AN: 994

South Asian (SAS) AF: 0.000569 AC: 1 AN: 1758

European-Finnish (FIN) AF: 0.000862 AC: 4 AN: 4642

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 176

European-Non Finnish (NFE) AF: 0.00130 AC: 47 AN: 36092

Other (OTH) AF: 0.00380 AC: 4 AN: 1054

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.1
DANN	Benign	0.58
PhyloP100		0.096

Splicing

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

Other links and lift over

dbSNP: rs11977641; hg19: chr7-36795424;