19-40851171-T-C

Variant names:

• chr19-40851171-T-C
• rs61663607
• ENST00000601627.1:n.118-40820T>C

Variant summary

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

The ENST00000601627.1(ENSG00000268797):​n.118-40820T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0925 in 150,644 control chromosomes in the GnomAD database, including 1,119 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 0.093 (1119 hom., cov: 30)
• Consequence: ENSG00000268797 ENST00000601627.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0130
• Publications: 12 publications found

Genes affected

ENSG00000268797 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.208 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000601627.1. 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
	ENSG00000268797	ENST00000601627.1	TSL:3	n.118-40820T>C		intron	N/A	ENSP00000469533.1	M0QY20

Frequencies

GnomAD3 genomes AF: 0.0925 AC: 13924 AN: 150530 Hom.: 1117 Cov.: 30

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0437

Gnomad ASJ AF: 0.0914

Gnomad EAS AF: 0.219

Gnomad SAS AF: 0.0684

Gnomad FIN AF: 0.144

Gnomad MID AF: 0.0924

Gnomad NFE AF: 0.0824

Gnomad OTH AF: 0.0842

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

GnomAD4 genome AF: 0.0925 AC: 13937 AN: 150644 Hom.: 1119 Cov.: 30 AF XY: 0.0948 AC XY: 6967 AN XY: 73468

African (AFR) AF: 0.104 AC: 4287 AN: 41050

American (AMR) AF: 0.0435 AC: 659 AN: 15148

Ashkenazi Jewish (ASJ) AF: 0.0914 AC: 316 AN: 3456

East Asian (EAS) AF: 0.219 AC: 1075 AN: 4914

South Asian (SAS) AF: 0.0693 AC: 327 AN: 4718

European-Finnish (FIN) AF: 0.144 AC: 1491 AN: 10378

Middle Eastern (MID) AF: 0.0925 AC: 27 AN: 292

European-Non Finnish (NFE) AF: 0.0824 AC: 5579 AN: 67704

Other (OTH) AF: 0.0835 AC: 173 AN: 2072

Alfa AF: 0.0892 Hom.: 114

Bravo AF: 0.0879

Asia WGS AF: 0.140 AC: 478 AN: 3428

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.0
DANN	Benign	0.32
PhyloP100		0.013

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs61663607;

hg19: chr19-41357076;