2-97250149-G-C

Variant names:

• chr2-97250149-G-C
• NM_001354587.1:c.5730G>C

Variant summary

Our verdict is Benign. The variant received -7 ACMG points: 0P and 7B. BP4_Strong BP6_Moderate BP7

The NM_001354587.1(ANKRD36):​c.5730G>C​(p.Leu1910Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: not found (cov: 15)
  • Exomes 𝑓: 0.0000021 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ANKRD36 NM_001354587.1 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.781
• Publications: 0 publications found

Genes affected

ANKRD36 (HGNC:24079): (ankyrin repeat domain 36)

ACMG classification

Our verdict: Benign. The variant received -7 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BP6: Variant 2-97250149-G-C is Benign according to our data. Variant chr2-97250149-G-C is described in ClinVar as Likely_benign. ClinVar VariationId is 2651167.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=0.781 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001354587.1. 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
	ANKRD36	NM_001354587.1	MANE Select	c.5730G>C	p.Leu1910Leu	synonymous	Exon 75 of 76	NP_001341516.1	A6QL64-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANKRD36	ENST00000420699.9	TSL:5 MANE Select	c.5730G>C	p.Leu1910Leu	synonymous	Exon 75 of 76	ENSP00000391950.4	A6QL64-1
	ANKRD36	ENST00000461153.7	TSL:5	c.5730G>C	p.Leu1910Leu	synonymous	Exon 75 of 75	ENSP00000419530.3	A6QL64-1
	ANKRD36	ENST00000652721.1		c.5730G>C	p.Leu1910Leu	synonymous	Exon 75 of 76	ENSP00000498611.1	A6QL64-1

Frequencies

GnomAD3 genomes Cov.: 15

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000207 AC: 1 AN: 483906 Hom.: 0 Cov.: 6 AF XY: 0.00000394 AC XY: 1 AN XY: 253904

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

African (AFR) AF: 0.00 AC: 0 AN: 13434

American (AMR) AF: 0.00 AC: 0 AN: 18296

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 15122

East Asian (EAS) AF: 0.00 AC: 0 AN: 20760

South Asian (SAS) AF: 0.00 AC: 0 AN: 30528

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 33572

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1946

European-Non Finnish (NFE) AF: 0.00000309 AC: 1 AN: 323636

Other (OTH) AF: 0.00 AC: 0 AN: 26612

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome Cov.: 15

ClinVar

ClinVar submissions

Significance: Likely benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.0
DANN	Benign	0.28
PhyloP100		0.78
Mutation Taster		=100/0	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		Details are displayed if max score is > 0.2

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

Other links and lift over

hg19: chr2-97915886;