1-102317816-T-C

Variant names:

• chr1-102317816-T-C
• rs1935268
• ENST00000447916.1:n.340-7488A>G

Variant summary

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

The ENST00000447916.1(ENSG00000233359):​n.340-7488A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.948 in 151,786 control chromosomes in the GnomAD database, including 68,459 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 0.95 (68459 hom., cov: 32)
• Consequence: ENSG00000233359 ENST00000447916.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.285
• Publications: 0 publications found

Genes affected

ENSG00000233359 (HGNC:58374):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.986 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
ENSG00000233359	ENST00000447916.1	n.340-7488A>G		intron_variant	Intron 4 of 5	3
ENSG00000233359	ENST00000656454.1	n.45-7488A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.948 AC: 143718 AN: 151666 Hom.: 68406 Cov.: 32

Gnomad AFR AF: 0.877

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.963

Gnomad ASJ AF: 0.991

Gnomad EAS AF: 0.757

Gnomad SAS AF: 0.923

Gnomad FIN AF: 0.999

Gnomad MID AF: 0.991

Gnomad NFE AF: 0.992

Gnomad OTH AF: 0.957

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

GnomAD4 genome AF: 0.948 AC: 143831 AN: 151786 Hom.: 68459 Cov.: 32 AF XY: 0.947 AC XY: 70219 AN XY: 74164

African (AFR) AF: 0.877 AC: 36391 AN: 41484

American (AMR) AF: 0.963 AC: 14624 AN: 15192

Ashkenazi Jewish (ASJ) AF: 0.991 AC: 3441 AN: 3472

East Asian (EAS) AF: 0.757 AC: 3898 AN: 5148

South Asian (SAS) AF: 0.922 AC: 4449 AN: 4826

European-Finnish (FIN) AF: 0.999 AC: 10552 AN: 10562

Middle Eastern (MID) AF: 0.993 AC: 292 AN: 294

European-Non Finnish (NFE) AF: 0.992 AC: 67252 AN: 67786

Other (OTH) AF: 0.957 AC: 2020 AN: 2110

Alfa AF: 0.972 Hom.: 4304

Bravo AF: 0.939

Asia WGS AF: 0.844 AC: 2930 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.7
DANN	Benign	0.81
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs1935268; hg19: chr1-102783372;