chr4-65869024-T-C

Variant names:

• chr4-65869024-T-C
• rs7697319
• ENST00000782773.1:n.149T>C

Variant summary

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

The ENST00000782773.1(ENSG00000248479):​n.149T>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 0.339 in 152,038 control chromosomes in the GnomAD database, including 8,889 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 0.34 (8889 hom., cov: 33)
• Consequence: ENSG00000248479 ENST00000782773.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 2 publications found

Genes affected

ENSG00000248479 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.347 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377259	XR_938834.2	n.149T>C		non_coding_transcript_exon_variant	Exon 2 of 4
LOC105377259	XR_938835.2	n.120T>C		non_coding_transcript_exon_variant	Exon 1 of 3
LOC105377259	XR_938836.2	n.144T>C		non_coding_transcript_exon_variant	Exon 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000248479	ENST00000782773.1	n.149T>C		non_coding_transcript_exon_variant	Exon 2 of 4
ENSG00000248479	ENST00000782774.1	n.244T>C		non_coding_transcript_exon_variant	Exon 2 of 5
ENSG00000248479	ENST00000782771.1	n.135+452T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.339 AC: 51483 AN: 151920 Hom.: 8876 Cov.: 33

Gnomad AFR AF: 0.352

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.345

Gnomad ASJ AF: 0.437

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.325

Gnomad FIN AF: 0.277

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.348

Gnomad OTH AF: 0.340

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

GnomAD4 genome AF: 0.339 AC: 51520 AN: 152038 Hom.: 8889 Cov.: 33 AF XY: 0.335 AC XY: 24868 AN XY: 74326

African (AFR) AF: 0.352 AC: 14599 AN: 41446

American (AMR) AF: 0.345 AC: 5269 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.437 AC: 1517 AN: 3468

East Asian (EAS) AF: 0.188 AC: 974 AN: 5172

South Asian (SAS) AF: 0.324 AC: 1565 AN: 4824

European-Finnish (FIN) AF: 0.277 AC: 2920 AN: 10558

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.348 AC: 23635 AN: 67970

Other (OTH) AF: 0.340 AC: 720 AN: 2116

Alfa AF: 0.345 Hom.: 1084

Bravo AF: 0.347

Asia WGS AF: 0.316 AC: 1100 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.78
DANN	Benign	0.32
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs7697319; hg19: chr4-66734742;