7-150342466-C-T

Variant names:

• chr7-150342466-C-T
• rs3735167
• ENST00000563946.1:n.696C>T

Variant summary

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

The ENST00000647589.1(ENSG00000301866):​n.413C>T 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 0.219 in 133,858 control chromosomes in the GnomAD database, including 3,611 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 0.22 (3609 hom., cov: 31)
  • Exomes 𝑓: 0.36 (2 hom.)
• Consequence: ENSG00000301866 ENST00000647589.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.280
• Publications: 25 publications found

Genes affected

ENSG00000301866 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.274 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000647589.1. 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
	ENSG00000301866	ENST00000563946.1	TSL:6	n.696C>T		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000301866	ENST00000647589.1		n.413C>T		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000301866	ENST00000782374.1		n.575C>T		non_coding_transcript_exon	Exon 1 of 3

Frequencies

GnomAD3 genomes AF: 0.219 AC: 29285 AN: 133788 Hom.: 3616 Cov.: 31

Gnomad AFR AF: 0.0775

Gnomad AMI AF: 0.398

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.316

Gnomad EAS AF: 0.287

Gnomad SAS AF: 0.287

Gnomad FIN AF: 0.254

Gnomad MID AF: 0.264

Gnomad NFE AF: 0.262

Gnomad OTH AF: 0.212

GnomAD4 exome AF: 0.364 AC: 8 AN: 22 Hom.: 2 Cov.: 0 AF XY: 0.357 AC XY: 5 AN XY: 14

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AC: 0 AN: 0

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

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.500 AC: 5 AN: 10

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.333 AC: 2 AN: 6

Other (OTH) AF: 0.500 AC: 1 AN: 2

GnomAD4 genome AF: 0.219 AC: 29266 AN: 133836 Hom.: 3609 Cov.: 31 AF XY: 0.220 AC XY: 14467 AN XY: 65790

African (AFR) AF: 0.0775 AC: 1913 AN: 24692

American (AMR) AF: 0.151 AC: 2201 AN: 14586

Ashkenazi Jewish (ASJ) AF: 0.316 AC: 1084 AN: 3430

East Asian (EAS) AF: 0.286 AC: 1476 AN: 5152

South Asian (SAS) AF: 0.287 AC: 1379 AN: 4804

European-Finnish (FIN) AF: 0.254 AC: 2667 AN: 10508

Middle Eastern (MID) AF: 0.246 AC: 67 AN: 272

European-Non Finnish (NFE) AF: 0.262 AC: 17721 AN: 67586

Other (OTH) AF: 0.209 AC: 397 AN: 1898

Alfa AF: 0.223 Hom.: 3569

Bravo AF: 0.176

Asia WGS AF: 0.259 AC: 897 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.93
DANN	Benign	0.49
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs3735167; hg19: chr7-150039555;